title: Characterization of the mouse transcriptome by Serial Analysis of Gene Expression

city: Québec

first: Kouamé Ettienne

last: Kouadjo

state: Québec

address: 2705 Bld Laurier

institute: Laval University

summary:
This study characterizes the expressed transcripts of 15 intact tissues in mice by using the serial analysis of gene expression (SAGE) strategy which indicates the relative level of expression for each transcript matched to the tag.
Keywords: double-strand cDNA , serial analysis of gene expression (SAGE) , ditags

overall_design: Total RNA was isolated from tissues by using the RNA extraction kit (TRIzol Reagent, Invitrogen Canada Inc., Burlington, ON). Approximately 5 µg of mRNA was extracted with Oligotex mRNA Mini Kit (Qiagen Inc., Mississauga, ON). The SAGE method was performed as previously described (Velculescu et al., 1995; St-Amand et al., 2001). In brief, double-strand cDNA was synthesized from the mRNA using a biotinylated (T)18 primer and cDNA synthesis kit (Invitrogen Canada Inc.). The cDNA libraries were digested with the restriction enzyme NlaIII (New England Biolabs Inc., Pickering, ON). The 3'-terminal cDNA fragments were captured using streptavidin-coated magnetic beads (Dynal, Biotech LLC, Brown Deer, WI). After ligation of 2 annealed linker pairs, the cDNA fragments were digested with BsmFI (New England Biolabs Inc.). The blunting kit from Takara Bio Inc. (Otsu, Japan) was used for the blunting and ligation of the two tag populations. The resulting ligation products were amplified by PCR and digested with NlaIII. The band containing the ditags was extracted from the 12% polyacrylamid gel. Using T4 ligase (Invitrogen Canada Inc.), the ditags were self-ligated to form concatemers that were cloned into SphI site of pUC19. White colonies were screened by PCR and agarose gel to select long inserts for automated sequencing (Applied Biosystems 3730, Foster City, CA). The sequence and occurrence of each tag were analyzed by the SAGEana program, which is a new version of SAGEparser.pl (Dinel et al., 2005).

first: Kouame-Ettienne

first: Mayumi

last: Yoshioka

first: Jonny

last: St-Amand


title: Localization and mechanism of S. pombe histone demethylases

status: Public on Mar 22 2007

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

country: USA

institute: University of Texas at Austin

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

summary:
We profiled the genomic localization of two histone demethylases, LSD1 and LSD2 using ChIP-on-chip. Deletions in LSD2 are lethal but not in LSD1, so we examined effect of an lsd1 deletion on genomewide expression levels and localization patterns of H3me2K4 and H3me2K9 relative to wild-type.
Keywords: mutant vs wild-type

overall_design: Each experiment (transcription or ChIP localization) was implemented as a reference design including a dye reversal. Additional statistical power is added by the fact that the all experimental spots on the array platform are printed in duplicate.

first: Fei

last: Lan

first: Mikel

last: Zaratiegui

first: Judit

last: Villen

middle: W

first: Andre

last: Verdel

first: Maite

last: Huarte

first: Yu-Jiang

last: Shi

first: Steve

last: Gygi

first: Danesh

last: Moazed

first: Robert

middle: A

last: Martienssen

first: Yang


title: DNA demethylation in the Arabidopsis genome

status: Public on Apr 02 2007

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

type: Methylation profiling by genome tiling array

summary:
Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals.  In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA.  Demethylation by DME is necessary for genomic imprinting and demethylation by a related protein, REPRESSOR OF SILENCING1, which prevents gene silencing in a transgenic background.  However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known.  Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes.  Mutations in DML genes lead to locus-specific DNA hypermethylation.  Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist.  Of loci demethylated by DML enzymes, >80% are near or overlap genes.  Genic demethylation by DML enzymes primarily occurs at the 5' and 3' ends, a pattern opposite to the overall distribution of WT DNA methylation.  Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation.
Keywords: whole genome profiling, DNA methylation, demethylase

overall_design: Both experiments were done using two channels per chip.  The two microarray experiments compared immunoprecipitated, methylated DNA to control genomic DNA.

first: Jon

last: Penterman

first: Daniel

last: Zilberman

first: Jin

middle: H

last: Huh

first: Tracy

last: Ballinger

first: Steven

middle: L

last: Fischer


title: Treated Lymphoid ES cell line

status: Public on Apr 01 2007

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary:
lymphoid Es cell line
Keywords: cDNA array, ES cells

overall_design:
DNA chip technology has been exploited for RNA expression profiling analyses. Close to genome-wide microarrays were used for identification of changes in gene expression levels in lymphoid ES cell line.
In total 15chip hybridisations were performed including 7 dye swap experiments.

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: Gene expression profiling in skeletal muscle after the intramuscular administration of a pharmaceutical vehicle

status: Public on Mar 27 2007

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

country: France

institute: INRA

summary:
The objective of this work was to identify genes with a variable expression profile during the course of a skeletal muscle degeneration and regeneration damage in pig. Using cDNA microarrays and repeated measurements performed in the same ten piglets, the expression profile of 1651 genes was investigated at 0, 6 and 48 hours, then 7 and 21 days after the induction of a local iatrogenic muscle damage. The main variations in gene expression were seen within the first 2 days after the induction of the muscle damage. However, among the 81 theoretically possible patterns of gene expression profiles, only 14 were found to occur. Finally, from the whole data analysis, eight genes with the best discriminant power have been highlighted from 2 patterns of gene expression profiles: two of those genes were up regulated at 6 hours whereas the remaining 6 genes were up regulated toward the end of the muscle damage kinetic.
Keywords: other

overall_design: Ten piglets were included in this study. Each animal received a series of 4 intramuscular administrations of propylene glycol randomly distributed into the Longissimus dorsi muscles at different time-intervals in order to finally obtain muscle lesions at 6 h, 2, 7 and 21 days after the IM administration. An additional non-injected site was used as control muscle tissue. Total RNA was isolated from each of the 50 muscle samples using a commercial kit, and controlled for quality and concentration using an AGILENT 2100 bioanalyzer. cDNA was synthesized and labelled from 5 µg total RNA by simultaneous reverse transcription of mRNA using SuperScriptTM II RNase H- Reverse Transcriptase and 33P-deoxy-CTP. Each muscle sample mRNA was hybridized at 68°C during 24 h to one array containing two duplicated parts. The arrays were then exposed to radioisotopic-sensitive imaging plates that were scanned thereafter with a phosphor imaging system at a 25 µm resolution. Hybridization images were quantified using a semi-automated software through a grid process with a fixed spot diameter. The output was then subjected to the data analysis process.

first: Pierre

middle: J

last: Ferré

first: Didier

last: Concordet

first: Magali

last: SanCristobal

first: Emmanuelle

last: Uro-Coste

first: Gwenola

last: Tosser-Klopp

first: Agnès

last: Bonnet

first: Pierre-Louis

last: Toutain

first: François

last: Hatey

first: Hervé

middle: P

last: Lefebvre

first: Jean-Pierre

last: Gau

first: Nadine

last: Gautier

first: Francis

last: Benne

first: Janine

last: Rallières

first: Christelle

last: Dantec

first: Philippe

last: Besse

first: Alain

last: Baccini

first: Sébastien

last: Déjean

first: Christèle

last: Robert-Granié


title: Molecular basis of gender and reproductive status in breeding zebrafish

city: Exeter

first: Eduarda

middle: M

last: Santos

state: Devon

address: Prince of Wales Road

department: School of Biosciences

country: United Kingdom

institute: University of Exeter

summary:
Sexual reproduction is a complex process involving multiple pathways. In this study, we aimed at investigating gene expression profiles underlying gender specificity in the zebrafish. To do so, we analyzed the transcriptome of the gonads of breeding fish and queried the gene expression profiles for significant differences between the genders and also between stages of gonad development. Major differences in gene expression profiles between genders were encountered at the level of the gonads. In addition, we identified biological processes associated with stage of sexual development in female gonads.
Keywords: gender and stage related gene expression

overall_design:
Sexually mature fish (6 males and 6 females) were kept in a 15L tank and allowed to breed naturally. After a 20-day period, fish were sacrificed humanly and one of the gonads were extracted, fixed in RNAlater (Ambion) and stored at -20oC until required for microarray analysis. The remaining gonad was fixed in Bouins for histological analysis of the gender and reproductive stage. RNA was extracted using the TRI reagent method followed by a LiCl precipitation (Sigma) according to the manufacturer's instructions. Total RNA was amplified and labeled using the Amino Allyl MessageAmp aRNA amplification kit (Ambion). A reference design was used for the array hybridizations. Array analysis was performed according to established protocols (described in Santos et al., 2006) and the data was extracted and queried for differences in gene expression profiles between genders and also between individuals within a gender and correlated with the
histological characteristics of the gonads.

first: Peter

last: Kille

first: Victoria

last: Workman

first: Charles

middle: R

last: Tyler


title: Repression of BCL-6 is required for the formation of human memory B cells in vitro

status: Public on Apr 03 2007

city: New York

first: Kathryn

last: Calame

state: NY

address: 701 W.168th Street, HHSC 1204

institute: Columbia University

summary:
Determine the expression pattern of in vitro cultured human centrocytes, plasma and memory B cells.
Keywords: Memory B cells, In vitro culture, Human

overall_design: Cy3-labelled lymphoma cell lines and Cy5-labelled treated sample were hybridized to a Lymphochip microarray.

first: Tracy

middle: C

last: Kuo

first: Arthur

last: Shaffer

first: Joseph

last: Haddad

first: Yong-Sung

last: Choi

first: Louis

last: Staudt


title: Knock out Nur77 - Gene regulation studies in different organs

first: Martin

last: Irmler

summary:
Nur77 is an orphan member of the nuclear receptor superfamily that is expressed in various types of cells and mediates diverse biological processes. The knock out Nur77 has a mutation in exon 2. Ligands of the nuclear receptor are unknown.
Keywords: Dual colour hybridisation on cDNA microarrays, Nur77, Knock out

overall_design: DNA chip technology has been exploited for RNA expression profiling analysis. Close to genome-wide microarrays were used for identification of changes in gene expression levels in lung, heart, spleen, testis, skeleton muscle, brown adipose tissue of Nur77-/- mice. 7 pooled mutant mice were hybridised in repetitions against a pool of 7 reference mice (Nur77+/+). In total 24 chip hybridisations were performed including 50% dye swap experiments.

first: Johannes

last: Beckers

first: Horsch

last: Marion

first: Klingenspor

last: Martin


title: Comparison of conventional target labelling to PCR and IVT amplified target populations

city: Dunedin

first: Robert

last: Day

state: Otago

address: Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

summary:
Our aim was to identify which stand alone amplification protocol performed best in our lab when the starting amount of total RNA was limited to 50 ng (A typical amount of total RNA we obtained by laser capture microdissection of tissues from silique samples). Since the quality of extracted RNA is very often tissue dependent and will affect the amplification efficiency, we decided to use total RNA extracted from whole siliques; better representing tissues targeted by LCM. We set out to compare two basic methods of RNA amplification, based on IVT and PCR.
Keywords: Comparison of target preparation regimes from limiting amounts of RNA

overall_design:
RNA was isolated from siliques during early (2-5 DAP) and late (6-10 DAP) stages of development. To help identify major alterations in the array data due to our target preparation protocols, the late stage RNA sample was spiked with 10% early stage sample (90%-late). In the absence of compression, the signals from the genes only expressed in the early sample should not be more than 10-fold higher than those obtained from the late sample. Conversely, the late sample should display a full range of differential expression. This design should result in the unamplified MA plots (plots of differential expression against intensity) having a distinctive asymmetrical shape.

Our study compared unamplified samples and three RNA amplification regimes; one-round IVT, two-round IVT and a PCR-based method. The unamplified treatments used 30 µg of total RNA followed by conventional labelling and hybridisation. The one round IVT amplifications were made from 5 µg of total RNA (a standard labelling procedure in many microarray experiments). The two round IVT and PCR regimes started from 50 ng of total RNA and would therefore be appropriate for use with LCM samples. The unamplified treatment involved duplicate hybridisations of the 90%-late sample against our early sample. For each of the amplification regimes, a single amplification of the 90%-late sample was hybridised against two independent amplifications of our early sample. In all hybridisations the early and 90%-late samples were consistently labelled with Cy5 and Cy3, respectively. This consistent labelling strategy for all 8 slides reduced variation between the microarrays due to dye bias and enabled us to focus on the variation arising from duplicate amplifications of a single early silique sample.

first: Les

last: Mcnoe

first: Richard

last: Macknight


title: Comparative genomic hybridization and physiological characterization of environmental E.coli

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

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

sample_organism:
Escherichia coli
Escherichia coli K-12

overall_design: gDNA from E.coli test strains was labeled with Cy-5 and hybridized against E.coli K12, reference strain, labeled with Cy-3. Hybridization, performed in Agilent proprietary buffer was performed for 17H at 60°C. Slides were then scanned in the Agilent scanner and extracted with Feature Extraction software. Background subtracted data were normalized for unequal incorporation or loading (LOWESS). Normalized data were then analyzed using GACK (Leonard et al, JID, 2003)

first: Julian

last: Ihssen

first: Elena

last: Grasselli

first: Claudio

last: Bassin

first: Patrice

last: Francois

first: Jean-Claude

last: Piffaretti

first: Wolfgang

last: Koster

first: Jacques

last: Schrenzel

first: Thomas

last: Egli


title: Pain microarray analysis 2

status: Public on Mar 21 2007

city: Baltimore

first: Svetlana

middle: I

last: Novikova

state: MD

address: 666 W. Baltimore st

department: Biomedical Sciences

institute: University of Maryland

summary:
Neonatal noxious insult produces a long-term effect on pain processing in adults. Rats subjected to carrageenan (CAR) injection in one hindpaw within the sensitive period develop bilateral hypoalgesia as adults. In the same rats, inflammation of the hindpaw, which was the site of the neonatal injury, induces a localized enhanced hyperalgesia limited to this paw.
This study revealed significant basal and inflammation-associated aberrations in the expression of multiple genes in the LDH of adult animals receiving CAR injection at P3 as compared to their expression levels in the LDH of animals receiving either no injections or CAR injection at P12. In particular, at baseline, twelve genes (representing GABA, serotonin, adenosine, neuropeptide Y, cholecystokinin, opioid, tachykinin and interleukin systems) were up-regulated in the bilateral LDH of the former animals. The baseline condition in these animals was also characterized by up-regulation of seven genes (encoding members of GABA, cholecystokinin, histamine, serotonin, and neurotensin systems) in the LDH ipsilateral to the neonatally-injured paw. The largest aberration in gene expression, however, was observed during inflammation of the neonatally injured hindpaws in the ipsilateral LDH, which included thirty-six genes (encoding numerous members of glutamate, serotonin, GABA, calcitonin gene-related peptide, neurotrophin, and interleukin systems). These findings suggest that changes in gene expression may be involved in the long-term nociceptive effects of neonatal noxious insult at the spinal level.
Keywords: neonatally injured paw, inflammation, carrageenan injection

overall_design: To gain an insight into the long-term molecular changes involved in the above-described long-term nociceptive effects of neonatal noxious insult at the spinal level, we performed DNA microarray analysis (using microarrays containing oligo-probes for 205 genes encoding receptors and transporters for glutamate, GABA, and amine neurotransmitters, precursors and receptors for neuropeptides, and neurotrophins, cytokines and their receptors) to compare gene expression profiles in the lumbar spinal dorsal horn (LDH) of adult (P60) male rats that received neonatal CAR treatment within (at postnatal day 3; P3) and outside (at postnatal 12; P12) of the sensitive period. The data were obtained both without inflammation (at baseline) and during complete Freund's adjuvant induced inflammation of the neonatally injured paw. The observed changes were verified by real-time RT-PCR.

first: Michael

middle: S

last: Lidow

first: Fang

last: He

first: Jie

last: Bai


title: Gene expression in Histone H1 variant deletion chicken DT40 mutant cell

city: Atlanta

first: Hideharu

last: Hashimoto

state: GA

address: 1510 Clifton

institute: Emory University

summary:
There are six histone H1 variant in chicken. 01H1/02H1/03H1/.10H1/H1L and H1R. In those variant we forcused on H1L and H1R those molecule were most similar H1 among six H1 variants. we established linker histone H1L and H1R deleted mutant in chicken B-cell derived DT40 cell and assay gene expression in normal condition in those mutant cells.
The detail charactalization of those mutant cell was published in Takami et al., BBRC 268, 501-508 (2000) and Hashimoto et al., DNA repair (2007)
Keywords: gene expression array-based, count

overall_design:
There are six linker histone H1 variant in chicken. Linker histone was thought to be general gene supplesser. We established linker histone H1 variant mutant in chicken B-cell derived DT40 cell, and analyze total protein by 2D-PAGE to  find up- or down- regulatd protein.  In these mutant, there are some up regulated protein expression and down regulated protein expression (Takami et al., BBRC 268, 501-508 (2000), PubMedID 10679234).
These 2D-PAGE experiment were limited at low density protein region, we use Affymetrix array to search the gene that were regulated specific linker histone H1 variant mutant.

We assayed total gene expression profile in H1L and H1R deleted mutant cells.
all mutant cells were cultured in normal culture condition in RPMI 1640 medium supplemented with 10 µM 2-mercaptoethanol, 10% FCS (Biowest) and 1% chicken serum (Gibco) at 39.5˚C. Total RNA were isolated from exponently growing DT40 cells.

first: Yasunari

last: Takami

first: Tatsuo

last: Nakayama

first: Yoichi

last: Shinkai


title: Natural variation in gene expression between normal human individuals studied using Hu800 cDNA microarrays

status: Public on Mar 18 2007

city: Delhi

first: Anu

last: Sharma

email: anukaush@gmail.com, ramuigib@gmail.com

state: Delhi

address: Mall Road, Near Jubilee Hall

department: Functional Genomics Unit,

country: India

institute: Institute of Genomics and Integrative Biology

summary:
Hu800 array has gene probes for signal transduction (322 genes), inflammatory responses (50 genes), chemokines and their receptors (12 genes) and Th1 and Th2 cytokines (20 genes). Along with these set of genes 325 genes have been selected based on their variation in expression levels between unrelated individuals as studied using Affymetrix HG U95Av2 arrays (Sharma et al, 2005).
Keywords: Natural variation in gene expression between humans

overall_design: Seven normal human individuals with age group of 22-34 years were recruited. These seven individuals comprised of three female individuals (F51, F52, F53) and four male individuals (M55, M56, M57 and M58). Ten pair wise comparisons were carried out between these unrelated individuals following a partial loop design

first: Samir

middle: K

last: Brahmachari

first: Srinivasan

last: Ramachandran


title: Hepatic stellate cells (HSC), quiescent and activated - influence of ltbp1-k.o. on activation in vitro

status: Public on Mar 31 2007

city: Cologne

first: Sebastian

last: Knoebel

address: Nattermannallee 1

institute: MiltenyiBiotec GmbH

summary:
Hepatic stellate cells (HSC) constitute the most important fibrogenic cell type during liver fibrosis. To analyse the different phenotypes of quiescent and activated cells, cells of 5 animals  were transdifferentiated in a well established in vitro transdifferentiaition assay and compared to freshly seeded, quiescent HSC. Gene expression profiling of quiescent and in vitro activated HSC revealed well known and new marker genes upregulated upon HSC activation. ltbp1 (latent transforming growth factor beta binding protein 1) is a crucial factor controlling the secretion and bioactivation of TGFß1. Using the data comparing quiescent and activated HSC, we were able to qualify the subtle but reproducible differences in gene expression observed when comparing activated ltbp1-deficient and activted wt HSC. ltbp1-deficient HSC showed a less fibrogenic phenotype after 6 days of in vitro transdifferentiation compared to the wt counterparts. The microarray data was indepently confirmed in vivo using an experimental model for the induction of liver fibrosis (ligation of the common bile duct). ltbp1-/- mice, after 4 weeks of bile obstruction, showed markedly reduced signs of liver fibrosis.
Keywords: gene expression profiling, analysyis of a fibrogenic cell type in the liver and the influence of ltbp1-k.o.

overall_design: Five mice per group were sacrificed and HSC were prepared by pronase/collagenase in situ perfusion. Cells wer pooled and seeded on plastic dishes. wt cells were cultured for one day (refered to as quiescent cells) or 6 days to induce transdifferentiation (refered to as activated cells). Cells from ltbp1 deficient animals were also cultured for 6 days to induce transdifferentiation. RNA was prepared thereafter, quantified and checked for integrity. Equal amounts of RNA (out of 5 animals per group) were subjected to linear amplification and labeling and used for hybridization on PIQOR_TM Microarrays. One microgram of RNA was labeled by reverse transcription via Cy3-dCTP (sample 1) and Cy5-dCTP (sample 2) incorporation. Both experiments (A: quiescent_wt_vs_activated_wt and B: activated_wt_vs_activated_ltbp1-/-) were conducted as technical replicates.

first: F

last: Drews

first: S

last: Knobel

first: M

last: Moser

first: K

middle: G

last: Muhlack

first: C

last: Stoll

first: A

last: Bosio

last: Gressner

first: R

last: Weiskirchen


title: Wild type versus PerR mutant Streptococcus pyogenes

city: St. Louis

first: Michael

last: Caparon

state: MO

address: 660 S. Euclid Ave.

department: Dept. of Molecular Microbiology

institute: Washington University School of Medicine

summary:
In Streptococcus pyogenes, mutation of the peroxide sensor PerR results in avirulence despite producing hyper-resistance to peroxide stress. To understand the basis of this effect, global transcription profiling was conducted.
Keywords: Study of the regulation of gene expression by PerR

overall_design:
A S. pyogenes genespecific microarray, consisting of 60 to 80-mer oligonucleotides representing 517 genes out of a total of 1752 predicted open reading frames in the SF370 genome, was constructed. S. pyogenes wild type strain (HSC5) or HdeltaPerR strain (PerR mutant derived form the wild type strain HSC5) were grown in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY medium) to mid-logarithmic phase of growth (OD600=0.3). RNA was extracted, amplified, and hybridized to the arrays.
Each experiment consisted of a pair-wise competitive hybridization of amplified RNA samples from the wild type and PerR mutant derived RNA. Since 2 biological replicates were tested in duplicate with a reciprocal dye-flip, a total of eight DNA microarrays were used for comparison for each set of RNA amplifications.

first: Audrey

last: Brenot

first: Seth

middle: D

last: Crosby


title: High-resolution genomic profiles of breast cancer cell lines

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

type: Genome variation profiling by genome tiling array

summary:
A BAC-array platform for comparative genomic hybridization was constructed from a library of 32,433 clones providing complete genome coverage, and evaluated by screening for DNA copy number changes in 11 breast cell lines (BT474, MCF7, HCC1937, SK-BR-3, L56Br-C1, ZR-75-1, MCF10A, JIMT1, MDA-MB-231, MDA-MB-361 and HCC2218). These were also characterized by gene expression analysis and found to represent all five recently described breast cancer subtypes using the ‘intrinsic gene set’ and centroid correlation. Three cell lines, HCC1937 and L56BrC1 derived from BRCA1 mutation carriers and MDA-MB-231, were of basal-like subtype and characterized by a high frequency of low-level gains and losses of typical pattern, including limited deletions on 5q. Four estrogen receptor positive cell lines were of luminal A subtype and characterized by a different pattern of aberrations and high-level amplifications, including ERBB2 and other 17q amplicons in BT474 and MDA-MB-361. SK-BR-3 cells, characterized by a complex genome including ERBB2 amplification, massive high-level amplifications on 8q and a homozygous deletion of CDH1 at 16q22, had an expression signature closest to luminal B subtype. The effects of gene amplifications were verified by gene expression analysis to distinguish targeted genes from silent amplicon passengers. JIMT1, derived from an ERBB2 amplified trastuzumab resistant tumor, was of the ERBB2 subtype. Homozygous deletions included other known targets such as PTEN (HCC1937) and CDKN2A (MDA-MB-231, MCF10A), but also new candidate suppressor genes such as FUSSEL18 (HCC1937) and WDR11 (L56Br-C1) as well as regions without known genes. The tiling BAC arrays constitute a powerful tool for high-resolution genomic profiling suitable for cancer research and clinical diagnostics.
Keywords: comparative genomic hybridization

overall_design: Genomic DNA was extracted from 11 breast cancer cell lines. The DNA was labeled using Bioprime array CGH labeling kit (Invitrogen). Promega pooled male DNA was used as reference. Dye-swaps were performed for L56Br-C1 and HCC2218. Labeled DNA was hybridized onto BAC arrays containing ~32 000 BAC clones printed in singlets. BAC arrays were produced at the SWEGENE DNA Microarray Facility at Lund University.

first: Göran

last: Jönsson

first: Eleonor

last: Olsson

first: Markus

last: Heidenblad

last: Vallon-Christersson

first: Kazutoyo

last: Osoegawa

first: Pieter

last: de Jong

first: Stina

last: Oredsson

last: Ringnèr

first: Mattias

last: Höglund

first: Ake

last: Borg


title: Shaping of Tumor and Drug Resistant Genomes by Instability and Selection

status: Public on Mar 16 2007

city: San Francisco

first: Antoine

last: Snijders

state: CA

address: 2340 Sutter Street

department: Cancer Research Institute

institute: University of California San Francisco

summary:
We used genome-wide microarray comparative genomic hybridization to carry out a higher resolution evaluation of the effect of MMR competence on genomic alterations occurring in 20 cell lines and to determine if characteristic aberrations arise in MMR proficient and deficient HCT116 cells undergoing selection for methotrexate resistance.
Keywords: Comparative Genomic Hybridization

overall_design: Array CGH experiments of cell line genomic DNA as test samples and normal human genomic DNA as reference sample.

first: Jane

last: Fridlyand

first: Dorus

last: Mans

first: Richard

last: Segraves

first: Ajay

last: Jain

first: Daniel

last: Pinkel

first: Donna

last: Albertson


title: Gene expression data of primary lung cancer

status: Public on Mar 30 2007

city: Chuo-ku, Chiba

first: YASUMITSU

last: MORIYA

address: 1-8-1, Inohana

department: Thoracic surgery

country: Japan

institute: Chiba University

summary:
We used microarrays to detail the clinical features in patients with lung cancer and identified genes differentially expressed between non-tumorous tissue and cancer  tissue of lung.
Keywords: disease state analysis

overall_design: A total of 100 surgical specimens of lung cancer tissues (63 adenocarcinomas, 22 squamous cell carcinomas, 10 large cell carcinomas, 3 small cell carcinomas, and 2 others) and corresponding non-tumor lung tissues were obtained from 37 female and 63 male patients who had consecutively undergone potentially curative resection at Chiba University Hospital. RNA was isolated from these specimens and gene expression profiles were analyzed using the AceGene Human Oligo Chip 30K Subset A.  For gene expression analysis of primary resected lung adenocarcinoma, we applied the expression data of 52 cases consisting of 32 adenocarcinoma and 20 non-adenocarcinoma cases. For gene expression analysis of primary resected lung squamous cell carcinoma, we applied the expression data of 52 cases consisting of 12 squamous cell carcinoma and 40 non-squamous cell carcinoma cases. For gene expression analysis of lymph node metastasis, we applied the expression data of 27 lung adenocarcinoma cases consisting of 12 lymph node-positive and 15 lymph node-negative cases.  For gene expression analysis of postoperative tumor recurrence, we applied the expression data of 40 lung adenocarcinoma cases consisting of 17 postoperative tumor recurrence, and 23 postoperative non-tumor recurrence cases.

first: Yasumitsu

last: Moriya

first: Akira

last: Iyoda

first: Yasuhiro

last: Kasai

first: Takashi

last: Sugimoto

first: Junya

last: Hashida

first: Yoshinori

last: Nimura

first: Masaki

last: Kato

last: Takiguchi

first: Naohiko

last: Seki

first: Takehiko

last: Fujisawa


title: miRNA profiling in Human K562 cells undergoing erythropoietic induction

city: Singapore

first: Meng Ling

last: Choong

address: 31 Biopolis Way, #03-01 Nanos

department: Drug Discovery

country: Singapore

institute: Experimental Therapeutics Centre

summary:
We investigated the miRNA expression in ex vivo human erythroid cultures from K562 cells.  Hypothetically, the decline of certain miRNAs may promote erythropoiesis by unblocking expression of key functional proteins while the up-regulation of other miRNAs may block commitment to non-erythroid lineages. By comparison with the miRNA expression changes in human umbilical cord blood-derived CD34 cells, signature miRNAs for erythroid development can be discovered.
Keywords: miRNA expression profiling

overall_design: Human K562 cell line was obtained from ATCC and maintained in IMDM with 10% fetal calf serum (Hyclone). For erythropoietic induction, the cells were adapted to the serum free defined media StemLineII (Sigma) first and then induced to differentiate in the StemLineII media supplemented with 50 ng/ml IL3 and 7.5 U/ml EPO (Mahdi et al. 1998). miRNAs were harvested at regular time points through out this period and hybridized onto the array.

first: MengLing

first: Henry

last: Yang

first: Ian

last: McNiece


title: Transcriptome analyses of narrow sheath shoot apical meristem (SAM) vs non-mutant SAM

status: Public on Mar 14 2007

city: Ithaca

first: Michael

last: Scanlon

address: 140 Emerson Hall

department: Department of Plant Biology

institute: Cornell University

summary:
Loss of function mutations in the narrow sheath (ns) duplicate genes (ns1 and ns2) cause the deletion of a mediolateral domain from maize leaves. The ns genes encode duplicate WUSCHEL1-like homeobox (WOX) putative transcription factors that function redundantly and non-cell autonomously to direct recruitment of leaf founder cell-initials in a lateral domain of the shoot apex. In order to investigate the genetic mechanisms of NS1 gene function, SAM-specific transcriptional profiling of narrow sheath mutant1-R comparing to that of nonmutant using laser microdissection microarray. Whole SAMs were laser-microdissected from ns1-R mutant and non-mutant seedlings grown under the same controlled conditions. Microarray profiles were generated for 37,662 maize cDNAs contained on gene chips SAM 1.1, SAM 2.0 and SAM 3.0 (For details, see the the Iowa State University Center for Plant Genomics website).
Keywords: Genetic modification

overall_design: Two-condition experiment, ns SAM vs non-mutant SAM cells. 6 Biological replicates with dye swaps. One replicate per array.

first: Xiaolan

last: Zhang


title: Monitoring Burma mangrove transcriptome changes in response to salt and osmotic stress.

status: Public on Mar 10 2007

city: Hachioji

first: Miyama

last: Masashi

state: Tokyo

address: Katakura 1404-1

department: School of Bionics

institute: Tokyo University of Technology

summary:
Generally, salt stress causes both osmotic and ionic stress. To discern the effects of osmotic and ionic specific effects on Burma mangrove transcriptome, we conducted expression profiling in 500 mM NaCl or 1M solbitol treated leaves. This study will lead to a rapid and effective selection of gene that confers high salt tolerance in transgenic plants and to a comprehensive understanding of plant stress response.
Keywords: Stress response

overall_design: The 19 hybridizations were carried out, 18 hybridizations in 6 conditions (NaCl treated for [0h, 6h, 1d], and Solbitol treated for [0h, 6h, 1d]) with 3 biological replicates [A,B,C] per condition) and 1 additional hybridization for the initial self- vs. self-hybridization to assess technical variability.

first: Masashi

last: Miyama

first: Nobutaka

last: Hanagata

first: Yuichi

last: Tada


title: Gene expression during oosporogenesis in Phytophthora

city: Riverside

first: Howard

last: Judelson

address: Boyce Hall

department: Plant Pathology

institute: University of California

summary:
A screen for genes induced during sexual development was performed in the heterothallic oomycete Phytophthora infestans, the potato blight agent.  Of 15,644 unigenes on the Affymetrix chip, 87 were induced >10-fold during mating, with 28 induced >100-fold.  This was subsequently validated in independent matings using RNA blots and RT-PCR.
Keywords: Developmental stage comparison

overall_design: RNA was harvested from nonmating cultures of an A1 mating type strain and an A2 mating type strain, and from mixtures of the A1 and A2 strains (3 and 10 day mating cultures).  For each treatment, triplicate cultures were prepared on different days. The RNA from the three replicates was pooled to make the probe for each of the four chips, thereby providing pseudobiological replicates but no technical replicates.

first: Waraporn

last: Prakob


title: Yeast magnesium starvation, 90 minutes

status: Public on Mar 08 2007

city: Vienna

first: Jochen

last: Stadler

address: Dr. Bohrgasse 9

department: Department of Genetics

country: Austria

institute: MFPL, University of Vienna

summary:
To learn about the cellular processes involved in Mg2+ transport and the mechanisms allowing cells to cope with low Mg2+ availability, we performed RNA expression profiling experiments, and followed changes in gene activity upon Mg2+ depletion on a genome-wide scale. A striking portion of genes up-regulated under Mg2+ depletion is also induced by high Ca2+ and/or alkalinization. Among the genes significantly up-regulated by Mg2+ starvation, Ca2+ stress and alkalinization are ENA1 (encoding a P-type ATPase sodium pump) and PHO89 (encoding a sodium/phosphate cotransporter). We show that up-regulation of these genes is dependent on the calcineurin/Crz1p signaling pathway. Similarly to Ca2+ stress, Mg2+ starvation induces translocation of the transcription factor Crz1p from the cytoplasm into the nucleus. The up-regulation of ENA1 and PHO89 upon Mg2+ starvation depends on extracellular Ca2+. Using fluorescence resonance energy transfer microscopy we demonstrate that removal of Mg2+ results in an immediate increase in free cytoplasmic Ca2+. This effect is dependent on external Ca2+. Results presented indicate that Mg2+ depletion in yeast cells leads to enhanced cellular Ca2+ concentrations, which activate the Crz1p/calcineurin pathway. We provide evidence that calcineurin/Crz1p signaling is crucial for yeast cells to cope with Mg2+ depletion stress.
Keywords: stress response (magnesium starvation)

overall_design:
Mg2+ starvation and RNA isolation - For each experiment two identical yeast cultures were grown in synthetic medium containing 1 mM MgCl2 to OD600 = 0.5. The cultures were centrifuged, washed twice with pre-warmed synthetic medium containing either 1 mM MgCl2 (+Mg2+) or no MgCl2 (-Mg2+), and resuspended in the same medium. For time course experiments aliquots were removed at the indicated time points; for all other experiments cells were harvested 70 minutes after the 1st wash. For the FK506 experiment, FK506 (Fujisawa GmbH, Munich) in DMSO was added to a final concentration of 1 µg/ml (=1.25 µM) 10 minutes before centrifugation, and for all subsequent steps. Total RNA was isolated using the hot acidic phenol method (1). For microarray experiments three chloroform extractions were performed instead of one.
DNA microarray analyses - Yeast DNA arrays were obtained from the Ontario Cancer Institute Microarray Centre. Reverse transcription, probe cleanup, and microarray hybridization were performed according to the manufacturer’s protocol. Two individual experiments including dye-swap were performed. Microarrays were read using an axon GenePix 4000B laser scanner (Axon Instruments) and analyzed with the GenePix Pro 3.0 software. The Saccharomyces Genome Database was used to extract the information on the genes regulated by Mg2+ starvation. The geneXplorer 2.0 : Megayeast site from Stanford University was used to search for genes induced under general stress conditions.

first: Gerlinde

last: Wiesenberger

first: Rudolf

last: Schweyen


title: Identification of molecular markers involved in glycopeptide resistance of S. aureus

status: Public on Mar 09 2007

first: FRANCOIS

last: Patrice

summary:
To unravel molecular targets involved in glycopeptide resistance, three isogenic strains of Staphylococcus aureus with different susceptibility levels to vancomycin or teicoplanin were subjected to whole-genome microarray-based transcription and quantitative proteomic profiling. Quantitative proteomics performed on membrane extracts showed exquisite inter-experimental reproducibility permitting the identification and relative quantification of >30% of the predicted S. aureus proteome.

In the absence of antibiotic selection pressure, comparison of stable resistant and susceptible strains revealed 94 differentially expressed genes and 178 proteins. As expected, only partial correlation was obtained between transcriptomic and proteomic results during stationary-phase. Application of massively parallel methods identified one third of the complete proteome, a majority of which was only predicted based on genome sequencing, but never identified to date. Several over‑expressed genes represent previously reported targets, while series of genes and proteins possibly involved in the glycopeptide resistance mechanism were discovered here, including regulators, global regulator attenuator, hyper‑mutability factor or hypothetical proteins. Gene expression of these markers was confirmed in a collection of genetically unrelated strains showing altered susceptibility to glycopeptides.

Our proteome and transcriptome analyses have been performed during stationary‑phase of growth on isogenic strains showing susceptibility or intermediate level of resistance against glycopeptides. Altered susceptibility had emerged spontaneously after infection with a sensitive parental strain, thus not selected in vitro. This combined analysis allows the identification of hundreds of proteins considered, so far as hypothetical protein. In addition, this study provides not only a global picture of transcription and expression adaptations during a complex antibiotic resistance mechanism but also unravels potential drug targets or markers that are constitutively expressed by resistant strains regardless of their genetic background, amenable to be used as diagnostic targets.
Keywords: Molecular markers, antibiotic resistance, glycopeptides, growth-phase

overall_design: Strains either sensitive or resistant to glycopeptides were grown separately. Total RNA extracted from stationary-phase culture were purified, labeled and hybridized in the Cy-3 channel against a pool of genomic DNA of strains used to design the microarray. We performed duplicate measurements for all conditions. The strains are MRGR3: parental strain, 14-4: Glycopeptide Intermediate S. aureus (GISA) and 14-4Rev: a revertant strain obtained from 14-4, susceptible to glycopeptides

first: Alexander

last: Scherl

first: Patrice

last: Francois

first: Yvan

last: Charbonnier

first: Jacques

last: Deshusses

first: Thibaud

last: Koessler

first: Antoine

last: Huyghe

first: Manuela

last: Bento

first: Jianru

last: Stahl-Zeng

first: Adrien

last: Fischer

first: Alexandre

last: Masselot

first: Alireza

last: Vaezzadeh

first: Francesca

last: Galle

first: Adriana

last: Renzoni

first: Pierre

last: Vaudaux

first: Daniel

last: Lew

first: Catherine

last: Zimmermann-Ivol

first: Pierre-Alain

last: Binz

first: Jean-Charles

last: Sanchez

first: Denis

middle: F

last: Hochstrasser

last: Schrenzel


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=0-100)

city: Zeist

first: Bart

last: Keijser

address: Utrechtseweg 48

country: Netherlands

institute: TNO

summary:
Bacillus subtilis forms dormant spores upon nutrient depletion. Under favorable environmental conditions, the spore breaks its dormancy and resumes growth in a process called spore germination and outgrowth. To elucidate the physiological processes that occur during the transition of the dormant spore to an actively growing vegetative cell, we studied this process in a time-dependent manner by a combination of microscopy, analysis of extracellular metabolites and a genome-wide analysis of transcription. The results indicate the presence of abundant levels of late sporulation transcripts in dormant spores. In addition, results suggest the existence of a complex and well-regulated spore outgrowth program, involving the temporal expression of at least 30 % of the B. subtilis genome.
Keywords: time course, spore outgrowth

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Time series of outgrowing B subtilis spores (cy-3) with common reference (RNA vegetative cells, TSB OD 0.4, Cy-5). Quality of the spotted oligoarray allows single dye dataanalysis.

first: Alex

last: Ter Beek

first: Han

last: Rauwerda

first: Frank

last: Schuren

first: Roy

last: Montijn

first: Hans

last: van der Spek

first: Stanley

last: Brul


title: Slc7a7 disruption causes fetal growth retardation by down-regulating Igf1 in the mouse model of LPI

city: brescia

first: andrea

last: bozzato

address: viale europa 11

country: Italy

institute: university of brescia

summary:
The solute carrier family 7A member 7 gene (SLC7A7) encodes the light chain of the heterodimeric carrier responsible for cationic amino acid (CAA) transport across the basolateral membranes of epithelial cells in intestine and kidney. Mutations affecting SLC7A7 cause lysinuric protein intolerance (LPI), a multiorgan disorder with clinical symptoms that include visceromegaly, growth retardation, osteoporosis, hyperammonemia, and hyperdibasicaminoaciduria. Here, we describe the consequences of inactivating Slc7a7 in a mouse model of LPI. The Slc7a7 mutation was generated by highthroughput retroviral gene-trapping in embryonic stem cells. The Slc7a7-/- mouse displayed intrauterine growth restriction (IUGR), commonly leading to neonatal lethality. After heavy protein ingestion, the surviving adult animals presented metabolic derangement consistent with that observed in human LPI. IUGR was investigated by examining the expression of main factors controlling fetal growth. Insulinlike growth factor 1, the dominant fetal growth regulator in late gestation, was markedly downregulated as demonstrated by quantitative real-time RT-PCR, immunostaining and Western blot analysis in fetal liver. To further explore the pathophysiology of LPI, gene expression profiling analyses were carried out by DNA microarray technology in intestine and liver of adult Slc7a7-/- mice. Significant up-regulation or down-regulation (two-fold or greater) was observed for 488 transcripts in intestine, and for 521 transcripts in liver. The largest category of differentially expressed genes corresponds to those involved in transport according to Gene Ontology classification. This mouse model offers new insights into the pathophysiology of LPI and into mechanisms linking CAA metabolic pathways and growth control. KEYWORDS: cationic amino acid transport; hyperdibasicaminoaciduria; neonatal lethality.
Keywords: Disease state analysis

overall_design: We directly compared Slc7a7 -/- mice versus normal control mice. For liver and intestine tissue, two sets of dye-swap experiments were performed, for a total of four replicate hybridizations for each tissue type.


title: Gene expression data from Mt/Gigi vs Mt root tissues

first: Maria

middle: J.

last: Harrison

address: Tower Road, Cornell Campus

institute: Boyce Thompson Institute for Plant Research

summary:
Most vascular flowering plants have the ability to form mutualistic associations with soil fungi from the Glomeromycota. The resulting symbiosis is called an arbuscular mycorrhiza and they are widespread in terrestrial ecosystems throughout the world. Significant alteration occurs at physiological and molecular levels in both symbionts. To gain a better understanding of the AM symbiosis, we use a 16000 feature oligonucleotide based array to examine gene expression in an arbuscular mycorrhizal symbioses, M. truncatula/Gigaspora gigantea.
Keywords: Medicago truncatula, Mycorrhizal, Gigaspora gigantea, microarray profiling

sample_organism:
Medicago truncatula
Gigaspora gigantea

overall_design: 28 days after inoculation, the Mt/Gigi and mock-inoculated (Mt) root tissues were harvested for RNA extraction and hybridized to the Medicago Genome Oligo Set Version 1.0 microarray. Six slides including three biological replicates and three dye-swap labeling replicates were hybridized for the experiment.

first: Jinyuan

last: Liu

first: Melina

last: Lopez-Meyer

first: Ignacio

last: Maldonado-Mendoza

first: Foo

last: Cheung

first: Christopher

last: Town


title: Gene expression data from Sh-Mt-Gi vs Mt shoot tissues

summary:
Most vascular flowering plants have the ability to form mutualistic associations with soil fungi from the Glomeromycota. The resulting symbiosis is called an arbuscular mycorrhiza and they are widespread in terrestrial ecosystems throughout the world. Although the physical interaction between the symbionts occurs in the root cortex, the symbiosis impacts the physiology of the whole plant. To gain a better understanding of the AM symbiosis, we have used the 16000 feature array to examine gene expression in the leaves of mycorrhizal plants to explore the transcriptional changes that are triggered systemically as a result of the AM symbiosis.
Keywords: Medicago truncatula, Mycorrhizal, systemic regulation, microarray profiling

overall_design: 30 days after inoculation, the shoot tissues from Mt/Gi and mock-inoculated (Mt) Medicago plants were harvested for RNA extraction and hybridized to the Medicago Genome Oligo Set Version 1.0 microarray. Six slides including three biological replicates and three dye-swap labeling replicates were hybridized for the experiment.


title: Genome-wide localization of ORC and MCM binding sites and identification of replication origins in S. pombe

status: Public on Mar 05 2007

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

summary:
DNA replication of eukaryotic chromosomes initiates at a number of discrete loci, called replication origins.  Distribution and regulation of origins are important for complete duplication of the genome.  Here, we determined locations of Orc1 and Mcm6, components of pre-replicative complex (pre-RC), on whole genome of Schizosaccharomyces pombe using a high-resolution tiling array.  Pre-RC sites were identified in 460 intergenic regions, where Orc1 and Mcm6 colocalized.  By mapping of 5-bromo-2’-deoxyuridine (BrdU)-incorporated DNA in the presence of hydroxyurea (HU), 307 pre-RC sites were identified as early-firing origins.  In contrast, 153 pre-RC sites without BrdU incorporation were considered to be late and/or inefficient origins.  Early and late origins tend to distribute separately in large chromosome regions.  Inactivation of replication checkpoint by deletion of Cds1 resulted in BrdU incorporation with HU specifically at the late origins.  An origin-exchange experiment showed that replication timing was not intrinsic to origin but dependent on its surrounding region.  Interestingly, pericentromeric heterochromatin and the silent mating type locus replicated in the presence of HU, while the inner centromere or subtelomeric heterochromatin did not.  Notably, MCM did not bind to inner centromeres where ORC was located.  Thus, replication is differentially regulated in chromosome domains.
Keywords: ChIP-chip analysis

overall_design:
Experiment Design:
•	The goal of the experiment –
 Genome-wide localization of ORC and MCM binding sites and identification of replication origins in Shizosaccaromyces pombe
•	A brief description of the experiment (e.g., the abstract from the related publication)
	DNA replication of eukaryotic chromosomes initiates at a number of discrete loci, called replication origins.  Distribution and regulation of origins are important for complete duplication of the genome.  Here, we determined locations of Orc1 and Mcm6, components of pre-replicative complex (pre-RC), on whole genome of Schizosaccharomyces pombe using a high-resolution tiling array.  Pre-RC sites were identified in 460 intergenic regions, where Orc1 and Mcm6 colocalized.  By mapping of 5-bromo-2’-deoxyuridine (BrdU)-incorporated DNA in the presence of hydroxyurea (HU), 307 pre-RC sites were identified as early-firing origins.  In contrast, 153 pre-RC sites without BrdU incorporation were considered to be late and/or inefficient origins.  Early and late origins tend to distribute separately in large chromosome regions.  Inactivation of replication checkpoint by deletion of Cds1 resulted in BrdU incorporation with HU specifically at the late origins.  An origin-exchange experiment showed that replication timing was not intrinsic to origin but dependent on its surrounding region.  Interestingly, pericentromeric heterochromatin and the silent mating type locus replicated in the presence of HU, while the inner centromere or subtelomeric heterochromatin did not.  Notably, MCM did not bind to inner centromeres where ORC was located.  Thus, replication is differentially regulated in chromosome domains.
•	Keywords, for example, time course, cell type comparison, array CGH (the use of MGED ontology terms is recommended).
	Mitosis, Cell cycle, Schizosaccharomyces pombe, Whole-genome, Tiling array, Chromosome II, III array, Orc1, Orc4, Mcm6, BrdU-labeling, cds1Δ.
•	Experimental factors
	Distribution of the Orc1 and Mcm6 in WT in G1 phase (S. pombe). Distribution of the Orc4 in WT in asynchronous cells (S. pombe). Distribution of BrdU-incorporated DNA in WT and in cds1 deletion mutant in S phase in the presence of HU (S. pombe).
•	Experimental design
	ChIP analysis: In all cases, hybridization data for ChIP fraction was compared with WCE (whole cell extract) fraction. Pombe whole-genome tiling array were used.
            BrdU analysis: Hybridization data for BrdU fraction (replicated DNA) was compared with Whole fraction (unreplicated DNA) or hybridization data for BrdU fraction of cds1Δ cells was compared with that of WT cells. Pombe whole-genome tiling array were used.

•	Quality control steps taken
	Different subunits of the same complex. Confirmation of several loci by q-PCR. Checking the BrdU-labeled DNA fraction in CsCl gradient by q-PCR or slot-blot analysis.
•	Links to the publication, any supplemental websites or database accession numbers.
GSE6523

Samples used, extract preparation and labelling:
•	The origin of each biological sample
	ChIP analysis: Schizosaccharomyces pombe nda3-KM311 cdc10-129 strain harboring pREP81-cdc18 and pREP42-cdt1.
            BrdU analysis: Schizosaccharomyces pombe wild type (cdc25-22 nmt1-TK) and cds1Δ strains.
•	Manipulation of biological samples and protocols used
	ChIP analysis: Chromatin immunoprecipitation (ChIP) in G1 arrested cells or asynchronous cells were performed as previously described (Takahashi et al., 2003, EMBO). Hybridization to Affimetrix high-density oligonucleotide array of S. pombe chromosomes 2 and 3 and whole genome tiling array of S. pombe was performed essentially as previously described (Katou et al., 2003, nature) (Lengronne et al., 2004, nature).
        BrdU analysis: Growing cdc25-22 cells expressing Thymidine Kinase were arrested at G2/M boundary and released in the presence of BrdU and HU. BrdU was incorporated in nascent DNA in following S phase. The genomic DNA was digested by HaeIII and BrdU-labeled DNA was purified in CsCl density gradient centrifugation. Hybridization to Affimetrix high-density oligonucleotide array of S. pombe whole genome tiling array was performed essentially as previously described (Katou et al., 2003, nature) (Lengronne et al., 2004, nature).

first: Makoto

last: Hayashi

first: Yuki

last: Katou

first: Takehiko

last: Itou

first: Mitsutoshi

last: Tazumi

first: Yoshiki

last: Yamada

first: Tatsuro

last: Takahashi

first: Takuro

last: Nakagawa

first: Hisao

last: Masukata


title: Gene expression of E. coli in continuous culture during adaptation to artificial sunlight

status: Public on Mar 20 2007

city: Bronx

first: Michael

last: Berney

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

summary:
E. coli growing in continuous culture under continuous UVA irradiation exhibits growth inhibition with a subsequent adaptation to the stress.  Transcriptome analysis was performed during transient growth inhibition and in the UVA light-adapted growth state.  The results indicate that UVA light induces stringent response and an additional response that includes the upregulation of the synthesis of valine, isoleucine, leucine, phenylalanine, histidine and glutamate.  The induction of several SOS response-genes strongly points to DNA damage as a result of UVA exposure.  The involvement of oxidative stress was observed with the induction of ahpCF.  Taken together it supports the hypothesis of the production of reactive oxygen species by UVA light.  In the UVA-adapted cell population strong repression of the acid tolerance response was found.  We identified the enzyme chorismate mutase as a possible chromophore for UVA light-inactivation and found strong repression of the pyrBI operon and the gene mgtA encoding for an ATP dependent Mg2+ transporter.  Furthermore, our results indicate that the role of RpoS may not be as important in the adaptation of E. coli to UVA light as it was implicated by previous results with starved cells, but that RpoS might be of crucial importance for the resistance under transient light exposure.
Keywords: stress response

overall_design: Slide microarrays were purchased from MWG-Biotech AG (Ebersberg, Germany). The MWG E. coli Array contains 4,288 gene specific oligonucleotide probes representing the complete E. coli K12 genome. Microarray slides were scanned using the Affymetrix 428TM Array Scanner (High Wycombe, UK). Spot intensities and corresponding background signals were quantified with the Affymetrix JaguarTM software version 2.0. Further data analysis was performed with the program GeneSpring from Silicon Genetics (Redwood City, CA, USA). Induction factors (IF) were calculated from the Cy3 and Cy5 signal intensities of the spot. Spots with signal intensity below a value of 50 were excluded from the analysis and the minimal induction factor was set to 0.01.  The normalization was performed with the 50th percentile distribution of remaining spots after background correction.  The mean value of the IF of a specific gene was calculated from three replicates.  Biological experiments were carried out three times, which provided three biological repeats. Dye swapping was performed for one replicate and did not alter the result.


title: Time series analysis of glucose-lactose diauxie: involvement of stringent response

status: Public on Mar 17 2007

city: Norman

first: Joe

last: Grissom

state: OK

address: 101 David L. Boren Blvd

department: Advanced Center for Genome Technology

institute: University of Oklahoma

summary: Guanosine 3 ,5 -bispyrophosphate (ppGpp), also known as ‘‘magic spot,’’ has been shown to bind prokaryotic RNA polymerase to down-regulate ribosome production and increase transcription of amino acid biosynthesis genes during the stringent response to amino acid starvation. Because many environmental growth perturbations cause ppGpp to accumulate, we hypothesize ppGpp to have an overarching role in regulating the genetic program that coordinates transitions between logarithmic growth (feast) and growth arrest (famine). We used the classic glucose-lactose diauxie as an experimental system to investigate the temporal changes in transcription that accompany growth arrest and recovery in wildtype Escherichia coli and in mutants that lack RelA (ppGpp synthetase) and other global regulators, i.e., RpoS and Crp. When cultured on a mixture of glucose and lactose, E. coli grows preferentially on glucose until it is exhausted, resulting in growth arrest while the cells adjust to growth on lactose, i.e., diauxie. Diauxie was delayed in the relA mutant and was accompanied by a 15% decrease in the number of carbon sources used and a  3-fold overall decrease in the induction of RpoS and Crp regulon  genes. Thus the data significantly expand the previously known  role of ppGpp and support a model wherein the ppGpp-dependent redistribution of RNA polymerase across the genome is the driving force behind control of the stringent response, general stress response, and starvation-induced carbon scavenging. Our conceptual model of diauxie describes these global control circuits as dynamic, interconnected, and dependent upon ppGpp for the efficient temporal coordination of gene expression that programs the cell for transitions between feast and famine.

overall_design: E. coli MG1655 and isogenic mutants were cultured in a 2 l Biostat B fermentor (B. Braun Biotech International) containing 1 liter of Morpholinepropanesulfonic acid (MOPS) minimal medium with 0.5 g/l of glucose and 1.5 g/l of lactose. The temperature was maintained at 37 ºC and pH was kept constant at 7.2 by the addition of 2 M NaOH. The dissolved oxygen level was maintained above 20% of saturation by adjusting the agitation speeds in the range of 270-500 rpm with fixed 1 l/min air flow.

first: M

last: Traxler

first: D

last: Chang

first: T

last: Conway

first: J


title: Dicer conditional knockout embryonic heart mutant vs control array

status: Public on Mar 24 2007

city: Houston

first: Ankang

last: Li

address: 2121 West Holcombe

department: CMDD

institute: IBT

summary:
The goal is to find out the gene expression changes when Dicer was inactivated in the murine heart.
Keywords: Dicer mutant

overall_design: Dicer gene was specifically inactivated in the mouse heart using cardiac specific Nkx2.5 Cre knock-in line. Embryonic day 11.5 heart from mutant and control hearts were  compared in triplicates.


title: UV timecourse

city: Wilmington

first: Ann

last: Stapleton

state: NC

address: 601 S. College

department: Biological Sciences

institute: University of North Carolina Wilmington

summary:
Transcriptome analysis of ultraviolet-radiation time course with paired treatment and control measurements provided groups of coordinately regulated genes and Gene Ontology processes.  A set of genes significantly affected by UV was selected by linear modeling plus order-restricted inference profile matches; this gene list was used to find upstream sequence motifs that predict UV regulation of gene expression.
Keywords: time course dose response stress response

overall_design:
A paired experimental design, with controls at each time point, was used to avoid confounding of UV-induced expression changes with circadian changes.  Plants were randomly assigned into control and experimental groups, and then subdivided into five groups of approximately 20 plants for treatments of one, two, four, eight, or twelve h of UV-B irradiation.  The experimental design incorporated four replicates of each of the five time points, with dye swap duplicates at each time point.  Thus, twenty maize cDNA Master Unigene slides were used.  Array hybridization was carried out using two samples per slide one sample was labeled with each dye. The following Samples were co-hybridized:

GSM101120 & GSM101130, GSM101127 & GSM101131, GSM101132 & GSM101128, GSM101133 & GSM101129, GSM101148 & GSM101152, GSM101184 & GSM101150, GSM101185 & GSM101151, GSM101186 & GSM101192, GSM101188 & GSM101196, GSM101197 & GSM101190, GSM101198 & GSM101191, GSM101201 & GSM101210, GSM101203 & GSM101211, GSM101212 & GSM101205, GSM101213 & GSM101207, GSM101214 & GSM101226, GSM101223 & GSM101227, GSM101228 & GSM101224, GSM101229 & GSM101225.

Key to sample labels:  The first word indicates the stress applied (either UV or no stress, indicated as treatment or controls) value.  The capital letter indicates the array channel and dye type for that sample (A for Cy3 and B for Cy5).  The lower-case letter is the replicate at each time point (a, b, c or d).  The final number is the time increment (1=1 hr, 2= 2 hr, 3=4 hr, 4=8hr, 5=12 hr).  The times were nested to avoid confounding.

first: Carletha

last: Blanding

first: Susan

last: Simmons

first: Paula

last: Casati

first: Virginia

last: Walbot

middle: E


title: Multiple classes of insecticides fail to induce the transcription of known detoxification gene families

city: Parkville

first: Lee

last: Willoughby

state: Victoria

address: 30 Flemington Road

department: Genetics

country: Australia

institute: University of Melbourne

summary:
Modifications of metabolic pathways are important in insecticide resistance evolution. Mutations leading to changes in expression levels or substrate specificities of cytochrome P450 (P450), glutathione-S-transferase (GST) and esterase genes have been linked to many cases of resistance with the responsible enzyme being shown to utilize the insecticide as a substrate.   Many studies show that the substrates of enzymes are capable of inducing the expression of those enzymes. We investigated if this was the case for insecticides and the enzymes responsible for their metabolism. The induction responses for P450s, GSTs and esterases to six different insecticides were investigated using a custom designed microarray in Drosophila melanogaster. Even though these gene families can all contribute to insecticide resistance, their induction responses by insecticides is minimal. The insecticides spinosad, diazinon, nitenpyram, lufenuron and dicyclanil did not induce any P450, GST or esterase gene expression. DDT was the only insecticide tested capable of eliciting an induction response, but only low levels for one GST and one P450. These results are in contrast to the induction responses observed for the natural plant compound caffeine and the barbituate drug phenobarbital, both of which induced a number of P450 and GST genes to high. Our results show that although insects evolve metabolic resistance to insecticides, induction does not usually have a role in survival after insecticide application, and induction studies cannot be used to predict which genes are capable of metabolizing insecticides. This has implications for managing the evolution of metabolic insecticide resistance in natural insect populations.
Keywords: induction response after treatment by various compounds

overall_design:
Drosophila melanogaster larvae were exposed to 7 different compounds and adult males were exposed to 2 different compounds.  For each compound 8 replicates of 50 individuals were exposed to the compound and an additional 8 replicates of 50 individuals were exposed to the appropriate control (that is the same exposure conditions, without the addition of the compound).
For each compound, RNA was extracted from all of the 8 samples and then pooled, before labelling.  For each experiment exposed/unexposed labelling dye swaps were used to account for potential differences in labelling efficiency.

first: Henry

last: Chung

first: Chris

last: Lumb

first: Charles

last: Robin

first: Philip

last: Batterham

first: Phillip

last: Daborn


title: Distribution of Arp4 in G2/M phase

city: Sendai

first: Hideaki

last: Ogiwara

state: Miyagi

address: Aoba 6-3,Aramaki-Aza,Aoba-ku

institute: Tohoku University

summary:
The actin-related proteins (ARPs) comprise a conserved protein family. Arp4p is found in large multisubunits of the INO80 and SWR1 chromatin remodeling complexes and in the NuA4 histone acetyltransferase complex. Here we show that arp4 (arp4S23AD159A) temperature-sensitive cells are defective in G2/M phase function. arp4 mutants are sensitive to the microtubule depolymering agent benomyl and arrest at G2/M phase at restrictive temperature. Arp4p is associated with centromeric and telomeric regions throughout cell cycle. Ino80p, Esa1p, and Swr1p, components of the INO80, NuA4, and SWR1 complexes, respectively, also associate with centromeres. The association of many kinetochore components including Cse4p, a component of the centromere nucleosome, Mtw1p, and Ctf3p is partially impaired in arp4 cells, suggesting that the G2/M arrest of arp4 mutant cells is due to a defect in formation of the chromosomal segregation apparatus.
Keywords: ChIP-chip

overall_design:
• The goal of the experiment
Genome-wide localization of Arp4 binding sites in Saccharomyces cerevisiae
• Experimental factors
Distribution of Arp4 in WT in G2/M phase in the presence of nocodazole (Saccharomyces cerevisiae).
• Experimental design
ChIP analysis: Hybridization data for ChIP fraction was compared with WCE (whole cell extract) fraction. Chromosome III, IV,V,VI S. cerevisiae: SC3456a520015F, P/N# 520015, affymetrix tiling array were used.

first: Ayako

last: Ui

first: Satoshi

last: Kawashima

first: Kazuto

last: Kugou

first: Fumitoshi

last: Onoda

first: Hitoshi

last: Iwahashi

first: Masahiko

last: Harata

first: Kunihiro

last: Ohta

first: Takemi

last: Enomoto

first: Masayuki

last: Seki


title: Array CGH in dendritic cell tumours

status: Public on Mar 15 2007

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

summary:
This series represents the data set described in the publication “Genetic and Immunohistochemical Analysis of Localized Extranodal and Nodal Dendritic Cell Tumours  – An Outlook for Individualized Therapies in Rare Tumours” by Ullmann et al. (submitted).
Keywords: array CGH

overall_design:
Six patients with dendritic cell tumors and one recurrence were hybridised on a submegabase resolution whole genome tiling path BAC array. DNA from two samples was isolated from frozen tissue, the remaining samples were available as formalin-fixed, paraffin embedded tissue only. Detailed step-by step protocols for labelling and hybridisation can be downloaded from our website.
Each case was hybridised once. No background subtraction was done and signal intensities were normalized by subgrid LOWESS. Circular binary segmentation was employed to define segments of the same DNA copy number change. Aberrations were defined as segments, which exceeded a fixed log2 threshold of +/- 0.2.

first: Ulrike

last: Gruber-Moesenbacher

first: Artur

last: Muradyan

first: Iris

last: Halbwedl

first: Kevin

middle: O

last: Leslie

first: Claus

last: Hultschig

first: Cord

last: Langner

first: Christine

last: Beham-Schmid

first: Helmut

last: Popper


title: Analgesia of naloxone in wild-type and NY1DD transgenic mouse model of sickle cell anemia using BMAP cDNA microarrays

city: Minneapolis

first: Ajay

last: Yekkirala

state: MN

address: 308 Harvard St 8-120

institute: University of Minnesota

summary:
Sickle cell disease is the most common genetic disorder in African-Americans. The opioid analgesic, morphine, has long been the treatment for the severe pain associated with this disease. Here we reveal that the opioid antagonist, naloxone, possesses potent analgesic activity in two strains of sickle cell mice (NY1DD and hBERK1) and not in their respective controls (ICR-CD1 and C57BL/6J) when administered by three parenteral routes. In the NY1DD sickle mice, naloxone (i.c.v.) possessed ~300-fold greater potency than morphine (i.c.v.). Other opioid antagonists (naltrexone, norbinaltorphimine, naltrindole) were substantially less effective in producing analgesia. Naloxone and morphine were synergistic in NY1DD mice, suggesting that analgesia was mediated via different receptor systems. Since microarray analysis suggested naloxone-induced down-regulation of the CCR5 chemokine receptor in NY1DD mice but not in control mice, the role of its endogenous ligand, CCL5 (RANTES), was investigated.
Keywords: Comparison of drug induced gene expression

overall_design:
In total 6 samples were analyzed. We used two strains of mice:
Wild-type: C57BL/6J
Sickle cell: NY1DD

To compare the gene expression patterns of naloxone 2 treatments were used:
i) Naloxone on sickle cell mice - 3 replicates
ii) Naloxone on wild-type mice - 3 replicates

As we used dual channel cDNA microarrays, the experimental (Cy5) channel was used for the naloxone and the control (Cy3) was always saline treated.

first: Mary

last: Lunzer

first: Robert

last: Hebbel

first: Philip

last: Portoghese


title: Profiling of Rgt1-regulated gene transcripts (30º C) in the fungal pathogen Candida albicans

status: Public on Mar 01 2007

city: Santa Barbara

first: Jessica

last: Sexton

address: UCSB/MCDB

institute: UCSB

summary:
C. albicans glucose sensing and signaling is important for full virulence in the mammalian host.  To better understand this phenomenon, we investigated the Hgt4 glucose-sensing pathway, focusing on the downstream transcriptional repressor CaRgt1.  CaRgt1-regulated gene transcripts were identified by comparing total RNA extracted from wild type and rgt1 mutant strains.  Cells were grown at 30 degrees C in the presence of glycerol, conditions under which CaRgt1 was expected to repress gene transcription.
Keywords: cell type comparison

overall_design:
A C. albicans genespecific microarray consisting of 70-mer oligonucleotides representing 6,346 of the 6,354 predicted ORFs in the annotated C. albicans genome assembly 19 was used.  Each ORF was represented by a specific oligonucleotide, and one genome equivalent of this oligo was spotted three times per slide.

To identify Rgt1-regulated transcripts, C. albicans cells from the wild type strain BWP17 or the rgt1 mutant strain CM18 were cultured in synthetic medium containing 5% glycerol at 30º C.  Cells were harvested and RNA was extracted, labeled, and hybridized to the arrays.  Each experiment consisted of a pair-wise competetive hybridization of total RNA samples derived from the wild type and mutant strains and included a reciprocal dye-flip replicate.  Since two biological duplicates were tested for each strain, a total of four DNA microarray slides were used.

Slides were scanned immediately after hybridization on a ScanArray express HT scanner (Perkin-Elmer).  The scanner photomultiplier tube (PMT) values were set for optimal intensity with minimal background.  An additional scan was done for each slide (low PMT) with the PMT such that <1% of the elements were saturated in order to characterise spots which were saturated at the higher PMT setting.

middle: A

first: Victoria

last: Brown

first: Mark

last: Johnston


title: Profiling of Rgt1-regulated gene transcripts (37º C) in the fungal pathogen Candida albicans

summary:
C. albicans glucose sensing and signaling is important for full virulence in the mammalian host.  To better understand this phenomenon, we investigated the Hgt4 glucose-sensing pathway, focusing on the downstream transcriptional repressor CaRgt1.  CaRgt1-regulated gene transcripts were identified by comparing total RNA extracted from wild type and rgt1 mutant strains.  Cells were grown at 37 degrees C in the presence of glycerol, conditions under which CaRgt1 was expected to repress gene transcription.
Keywords: cell type comparison

overall_design:
A C. albicans genespecific microarray consisting of 70-mer oligonucleotides representing 6,346 of the 6,354 predicted ORFs in the annotated C. albicans genome assembly 19 was used.  Each ORF was represented by a specific oligonucleotide, and one genome equivalent of this oligo was spotted three times per slide.

To identify Rgt1-regulated transcripts, C. albicans cells from the wild type strain BWP17 or the rgt1 mutant strain CM18 were cultured in synthetic medium containing 5% glycerol at 37º C.  Cells were harvested and RNA was extracted, labeled, and hybridized to the arrays.  Each experiment consisted of a pair-wise competetive hybridization of total RNA samples derived from the wild type and mutant strains and included a reciprocal dye-flip replicate.  Since two biological duplicates were tested for each strain, a total of four DNA microarray slides were used.

Slides were scanned immediately after hybridization on a ScanArray express HT scanner (Perkin-Elmer).  The scanner photomultiplier tube (PMT) values were set for optimal intensity with minimal background.  An additional scan was done for each slide (low PMT) with the PMT such that <1% of the elements were saturated in order to characterise spots which were saturated at the higher PMT setting.


title: Maternal MicroRNAs are Essential for Mouse Zygotic Development

city: Cambridge

first: Fuchou

last: Tang

state: Cambridgeshire

address: Tennis Court Road

department: Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

summary:
MicroRNAs (miRNAs) have been shown to have important functions in a variety of cellular processes. Here we report on miRNA expression and their dynamic regulation during mouse oogenesis and early embryos. We show that following specific deletion of Dicer from growing oocytes, the mutant oocytes cease development and were unable to progress through the first cell division. While the mutant mature oocytes seemed morphologically normal, they had disorganized spindle. Using detailed single cell cDNA microarray analysis of normal versus mutant oocytes, we found that a large proportion of maternal genes, including C-mos, are under the control of miRNAs. This study provides strong evidence that maternal miRNAs are essential for the earliest stages of mouse embryonic development.
Keywords: mRNA and miRNA expression comparison

overall_design: mRNA expression was compared with miRNA expression in dicer knockout and wild-type mouse mature oocyte.

first: Tang

last: Fuchou

first: Kaneda

last: Masahiro


title: Array CGH reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in Fallopian tube carcinoma

status: Public on Mar 06 2007

city: San Francisco

first: Antoine

last: Snijders

address: 2340 Sutter Street

institute: University of California San Francisco

summary:
Fallopian tube carcinoma (FTC) is a rare, poorly studied and aggressive cancer, associated with poor survival.  Since tumorigenesis is related to acquisition of genetic changes, we used genome-wide array CGH to analyze copy number aberrations occurring in FTC in order to obtain a better understanding of FTC carcinogenesis and to identify prognostic events and targets for therapy.  We used arrays of 2464 genomic clones, providing ~1.4 Mb resolution across the genome to quantitatively map genomic DNA copy number aberrations from fourteen FTC onto the human genome sequence.  All tumors showed a high frequency of copy number aberrations with recurrent gains on 3q, 6p, 7q, 8q, 12p, 17q, 19 and 20q, and losses involving chromosomes 4, 5q, 8p, 16q, 17p, 18q and X.  Recurrent regions of amplification included 1p34, 8p11-q11, 8q24, 12p, 17p13, 17q12-q21, 19p13, 19q12-q13 and 19q13.  Candidate, known oncogenes mapping to these amplicons included CMYC (8q24), CCNE1 (19q12-q21) and AKT2 (19q13), whereas PIK3CA and KRAS, previously suggested to be candidate driver genes for amplification mapped outside copy number maxima on 3q and 12p, respectively.  The FTC were remarkably homogeneous, with some recurrent aberrations occurring in more than 70% of samples, which suggests a stereotyped pattern of tumor evolution.
Keywords:  array CGH, CCNE1, AKT2, Fallopian tube cancer

overall_design: Here, we report on the application of array CGH to further refine regions of recurrent aberration in Fallopian Tube Carcinoma.

first: Marlies

last: Nowee

first: Jane

last: Fridlyand

first: Jurgen

last: Piek

first: Josephine

last: Dorsman

middle: N

last: Jain

first: Daniel

last: Pinkel

first: Paul

last: van Diest

first: Renee

middle: H

last: Verheijen

first: Donna

last: Albertson


title: Ptdsr-/- (phosphatidylserine receptor) fibroblasts

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary:
Phagocytosis of apoptotic cells is fundamental to animal development, immune function and cellular homeostasis. The phosphatidylserine receptor (Ptdsr) on phagocytes has been implicated in the recognition and engulfment of apoptotic cells and in anti-inflammatory signaling. Ptdsr is essential for the development and differentiation of multiple organs during embryogenesis. Ptdsr may thus have a novel, unexpected developmental function as an important differentiation-promoting gene. Moreover, Ptdsr is not required for apoptotic cell clearance by macrophages but seems to be necessary for the regulation of macrophage cytokine responses.
Keywords: ptdsr, fibroblast, cDNA microarray experiments,

overall_design: Comparison of Ptdsr-/- and Ptdsr+/+ fibroblasts in 14 chip experiments including 2 biological replicates (2 different fibroblast cell culture samples) and 50% dye swap experiments.

first: Johannes

last: Beckers

first: Marion

last: Horsch

first: Andreas

last: Lengeling

first: Jens

last: Böse


title: Neuronal differentiation of ES cells

first: Xin

last: Chen

institute: UCSF

summary:
The purpose of this study was to examine global gene expression during the differentiation of human embryonic stem cells to more restricted neural progenitors.  We developed an adherent differentiation protocol with completely defined media that produced 2 distinct classes of neuroepithelia based on timing, morphology and expression of known neural markers.  The first stage of differentiation is undifferentiated human ES cells (hESCs).  The second stage is aggregates of these hESCs after 6 days of separation from supportive mouse embryonic fibroblasts.  The third stage is a primitive anterior neuroepithelia that arises after 10 days of differentiation and is marked by a columnar morphology, expression of Pax6 and anterior neural patterning genes.  The fourth stage peaks at 17 days when cells form rosettes that resemble the neural tube and express the pan-neural marker Sox1.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Using regression correlation


title: Gene expression data from Mt/Gi vs Mt root tissues

city: Ithaca

first: Maria

last: Harrison

summary:
Most vascular flowering plants have the ability to form mutualistic associations with soil fungi from the Glomeromycota. The resulting symbiosis is called an arbuscular mycorrhiza and they are widespread in terrestrial ecosystems throughout the world. Significant alteration occurs at physiological and molecular levels in both symbionts. To gain a better understanding of the AM symbiosis, we use a 16000 feature oligonucleotide based array to examine gene expression in an arbuscular mycorrhizal symbioses, M. truncatula/G. intraradices.
Keywords: Medicago truncatula, Mycorrhizal, Glomus intraradices, microarray profiling

sample_organism:
Medicago truncatula
Rhizophagus intraradices

overall_design: 30 days after inoculation, the Mt/Gi and mock-inoculated (Mt) root tissues were harvested for RNA extraction and hybridized to the Medicago Genome Oligo Set Version 1.0 microarray. Six slides including three biological replicates and three dye-swap labeling replicates were hybridized for the experiment.

first: Jinyuan

last: Liu

first: Melina

last: Lopez-Meyer

first: Ignacio

last: Maldonado-Mendoza

first: Foo

last: Cheung

first: Christopher

last: Town

middle: J


title: Genome-wide assessment of DNA aberrations in human neuroblastoma primary tumors using BAC array

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

institute: Childrens Hospital of Philadelphia

summary:
DNA signature patterns embed important prognostic information in diagnostic neuroblastoma samples, and can identify candidate cancer-related genes.
Keywords: aCGH

overall_design: Measure DNA copy number alterations in a carefully annotated and representative set of 82 neuroblastoma tumors obtained at diagnosis on a customized high-resolution BAC array-based aCGH platform supplemented with additional clones at tiling path density across 1p36, 2p24, 3p21-22, 11q14-24, and 16p12-13, and integrate these data with genome-wide RNA expression data from the same tumors.


title: High resolution mapping reveals links of HP1 with active and inactive chromatin components

status: Public on Mar 02 2007

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

summary:
Heterochromatin protein 1 (HP1) is commonly seen as a key factor of repressive heterochromatin, even though a few genes are known to require HP1-chromatin for their expression. In order to obtain insight into the targeting of HP1 and its interplay with other chromatin components, we have mapped HP1 binding sites on chromosome 2 and 4 in Drosophila Kc cells using high-density oligonucleotide arrays and the DamID technique. The resulting high-resolution maps show that HP1 forms large domains in pericentric regions, but is targeted to single genes on chromosome arms. Intriguingly, HP1 shows a striking preference for exon-dense genes on chromosome arms. Furthermore, HP1 binds along entire transcription units, except for 5’ regions. Comparison with expression data shows that most of these genes are actively transcribed. HP1 target genes are also marked by the histone variant H3.3 and dimethylated histone 3 lysine 4 (H3K4me2), which are both typical of active chromatin. Interestingly, H3.3 deposition, which is usually observed along entire transcription units, is limited to the 5’ ends of HP1-bound genes. Thus, H3.3 and HP1 are mutually exclusive marks on active chromatin. Additionally, we observed that HP1-chromatin and Polycomb-chromatin are non-overlapping, but often closely juxtaposed, suggesting an interplay between both types of chromatin. These results demonstrate that HP1-chromatin is transcriptionally active and has extensive links with several other chromatin components.
Keywords: DamID

overall_design: DamID was performed for the heterochromatin protein HP1. Using high density oligonucleotide arrays we were able to map the binding sites of HP1 with a 100 bp resolution. Three biological replicates were analyzed, with one experiment in the reversed dye orientation.

first: Elzo

last: de Wit

first: Frauke

last: Greil


title: Comparison of normal and heat shock trophozoites

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

summary:
We examined the stress response in Entamoeba histolytica trophozoites by comparing untreated log-phase HM-1:IMSS trophozoites to those subjected to heat shock at 42C for 1 hour.
Keywords: stress reponse

overall_design: We compared two arrays from normal trophozoites to two arrays from trophozoites subjected to heat shock.

first: Jason

last: Hackney

first: Upinder

last: Singh


title: expression profiling of wild type and the hy5 mutant in arabidopsis

city: New Haven

first: Kun

last: He

state: CT

address: 165 Prospect

department: Molecular, Cellular & Developmental Biology

institute: Yale University

summary:
To determine the functional relevance of the HY5 binding sites to the transcriptional regulation, we performed genome wide expression analysis using WT and hy5 grown in continuous white light for 4 days.
Keywords: mutant/widetype comparative

overall_design: For this analysis, we used 70mer oligo microarray that covers 25,676 unique genes (Ma et al. 2005). Four biological replicate experiments were done with dye-swap design.

first: Jungeun

last: Lee

first: Ilha

first: Xingwang

last: Deng


title: Caco-2 incubation with different doses of Lactobacillus

city: Zeist

first: Sonia

last: Pavan

address: Utrechtseweg 48

department: Physiological Sciences

institute: TNO Quality of Life

summary:
Background: Lactobacillus plantarum is found in a variety of fermented foods and as such, consumed for centuries. Some strains are natural inhabitants of the human gastro-intestinal tract and like other Lactobacillus species, L. plantarum has been extensively studied for its immunomodulatory properties and its putative health-promoting effects (probiotic). Being the first line of host defense intestinal epithelial cells (IEC) are key players in the recognition and initiation of responses to gut microorganisms.
Results: Using high-density oligonucleotide microarrays we examined the gene expression profiles of differentiated Caco-2 cells exposed to various doses of L. plantarum. In addition, the effects were correlated to monolayer permeability studies and measurement of lactic acid production. A transcriptional dose-dependent IEC response to L. plantarum was found. Incubation of Caco-2 with a low bacterial dose induced a specific response, not due to cytotoxicity or production of lactic acid, including modulation of cell cycle and cell signaling functions. Exposure of Caco-2 cells to larger amounts of bacteria, accompanied by the production of lactic acid and glucose depletion, provoked increased permeability and supposed non-specific defense responses.
Conclusions: These results suggest that IEC are able to sense and react to the presence of gut bacteria. This study provides the first description of global transcriptional response of human IEC to a commensal lactic acid bacterium, and it shows the importance of choosing physiological bacterial doses to prevent the observation of non-specific host reactions.
Keywords: host-microbe interaction; dose response; transcriptional analysis

overall_design: Caco-2 cells were exposed for 10h to Lactobacillus. Fourteen samples are analyzed: 4 control Caco-2, 4 Caco-2 exposed to a low dose (10) of Lactobacillus, 4 Caco-2 exposed to a medium dose (100) of Lactobacillus, 2 Caco-2 exposed to a high dose (1000) of Lactobacillus. All 14 RNA samples are labeled with Cy5 and hybridized to a common reference (undifferentiated Caco-2, untreated) RNA labeled with Cy3

first: Johannes

last: van de Sandt

first: Michiel

last: Kleerebezem


title: Ptdsr (phosphatidylserine receptor) embryos

first: Martin

last: Irmler

summary:
Phagocytosis of apoptotic cells is fundamental to animal development, immune function and cellular homeostasis. The phosphatidylserine receptor (Ptdsr) on phagocytes has been implicated in the recognition and engulfment of apoptotic cells and in anti-inflammatory signaling. Ptdsr is essential for the development and differentiation of multiple organs during embryogenesis but not for apoptotic cell removal. Ptdsr may thus have a novel, unexpected developmental function as an important differentiation-promoting gene. Moreover, Ptdsr is not required for apoptotic cell clearance by macrophages but seems to be necessary for the regulation of macrophage cytokine responses.
Keywords: ptdsr, embryo E11.5, E12.5, E13.5, cDNA microarray experiments

overall_design: Comparison of Ptdsr-/- and Ptdsr+/+ embryos, age: E.11.5, E.12.5, E.13.5, technical replicates for all including 50% dye swap experiments. Biolobical replicates for E.12.5 only

last: Beckers

first: Marion

last: Horsch

first: Andreas

last: Lengeling

first: Jens

last: Böse


title: Gene expression signatures that predict radiation exposure (human)

city: Durham

first: Holly

middle: Kloos

last: Dressman

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University Medical Center

summary:
Gene expression analysis of peripheral blood leukocytes (PB MNCs) to develop expression profiles that accurately reflect prior radiation exposure.
Keywords: Comparative, exposure dosage, C57BI6 Murine Irradiation Studies, valdiation in human patients

overall_design:
We have made use of gene expression analysis of peripheral blood mononuclear cells (PB MNCs) to develop expression profiles that accurately reflect prior radiation exposure. Importantly, we demonstrate that expression profiles can be developed that not only predict radiation exposure in mice but also distinguish the level of radiation exposure, ranging from 50 cGy to 1000 cGy. Likewise, a molecular signature of radiation response developed solely from irradiated human patient samples can predict and distinguish irradiated human PB samples from non-irradiated samples with an accuracy of 90%, sensitivity of 85% and specificity of 94%. We further demonstrate that a radiation profile developed in the mouse can correctly distinguish PB samples from irradiated and non-irradiated human patients with an accuracy of 77%, sensitivity of 82% and specificity of 75%. Taken together, these data demonstrate that molecular profiles can be generated which are highly predictive of different levels of radiation exposure in mice and humans.
Homo sapiens
Human dataset only

first: Garrett

last: Muramoto

first: Nelson

last: Chao

first: Sarah

last: Meadows

first: Dawn

last: Marshall

first: Geoffrey

last: Ginsburg

first: Joseph

last: Nevins

first: John

middle: P

last: Chute


title: Expression data of E. histolytica trophozoites treated with 5AzaC

first: Gretchen

last: Ehrenkaufer

summary:
Expression profiling of treatment of E. histolytica HM-1:IMSS trophozoites with 5-Aza cytidine, an inhibitor of DNA methyltransferase
Keywords: drug treatment

overall_design: HM1 trophozoites were treated for 3 or 7 days with 23 micromolar 5-Aza cytidine, and RNA extracted and analyzed on a custom  Affymetrix array. Data from these two arrays is to be compared to expression data from HM1 trophozoites grown without drug exposure.

first: Ibne

last: Ali

middle: M

first: Jason

last: Hackney

first: Upinder

last: Singh


title: Analysis of transcription factor HY5 genomic binding sites in Arabidopsis

first: Kun

last: He

summary:
The transcription factor HY5 acts downstream of multiple families of the photoreceptors and promotes photomorphogenesis. Although it is well accepted that HY5 acts to regulate target gene expression, in vivo binding of HY5 to any of its target gene promoters has yet to be demonstrated. Here we used a chromatin immunoprecipitation procedure to verify suspected in vivo HY5 binding sites. We demonstrated that in vivo association of HY5 with promoter targets is not altered under distinct light qualities or during light-to-dark transition. Coupled with DNA chip hybridization using high density 60-nucleotide oligomer microarray that contains one probe for every 500 nucleotides over the entire Arabidopsis genome, we mapped genome wide in vivo HY5 binding sites. This analysis showed that HY5 binds preferentially to promoter regions in vivo and revealed over 3 thousand chromosomal sites as putative HY5 binding targets. HY5 binding targets tend to be enriched in the early light responsive genes and transcription factor genes. Our data thus supports a model in which HY5 is a high hierarchical regulator of the transcriptional cascades for photomorphogenesis.
Keywords: ChIP-chip

overall_design: To determine the in vivo HY5 binding sites in Arabidopsis genome, four biological ChIP-chip replicate assays were performed using HA specific antibody for HA:HY5 lines. The DNA from each ChIP was labeled with Cy5 and the sonicated input DNA was labeled with Cy3, and the pooled probes were used for hybridization with 60mer probes on a microarray chip that covers the sequenced Arabidopsis genome.

first: Jungeun

last: Lee

first: Ilha

first: Xing-wang

last: Deng