status: Public on Dec 23 2008

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

summary:
Identification of ANAC059 and ANAC092 early target genes using inducible overexpression system coupled with investigation of T-DNA insertion mutants
The aim was to identify early target genes of two senescence-associated transcription factors: ANAC059 and ANAC092. For this purpose we used estradiole-inducible system and studied the expression profile 5h after treatment using Affymetrix microarray. Additionally expression profile of  T-DNA insertion lines for ANAC059, ANAC092 and the wild-type were also analyzed.
Arabidopsis three weeks old transgenic plants (inducible overexpression)  were treated with estradiole for 5h. Based on our preliminary expriments we could identify that 5-h treatment is the shortest time point which result to the induction of ANAC092 and ANAC059 in inducible ANAC092 and ANAC059 overexpression plants, respectively. Additionally leaves of 38 days old plants  were harvest in T-DNA insertion lines of ANAC059, ANAC92 and the wild-type and expression profile was performed.

Keywords: genetic modification

overall_design: 3weeks old Arabidopsis ANAC059 and ANAC092 estradiole-induced overexpresion plants were treated with estradiole for 5h. As control, empty vector transgenic plants were also treated as same condition. Shoots of treated plants were harvested in order to RNA extraction and hybridization to affymetrix GeneChip array. For T-DNA insertion mutants, leaf number 11 were harvested 38 days old wt and mutant plants.

first: Bernd

last: Mueller-Roeber


title: Genome-wide analysis of alternative pre-mRNA splicing of the Drosophila hnRNP A/B family members

status: Public on Dec 30 2008

city: Kansas City

first: Marco

last: Blanchette

state: MO

country: USA

institute: Stowers Institute for Medical Research

type:
Other
Expression profiling by array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression data for biophenotypic leukemia patients treated in St. Jude Children's Research Hospital

status: Public on Jan 06 2009

city: Memphis

first: Xueyuan

last: Cao

state: TN

address: 262 Danny Thomas Place

department: Biostatistics

institute: St Jude Children's Research Hospital

summary:
Mixed-lineage leukemias represent about 3-5% of acute leukemias occurring in patients of all ages and comprise several different subtypes (biphenotypic, bilineal, and lineage switch). The optimal therapeutic approach to these cases, especially in pediatric patients, has not been defined. We used microarrays to detail the gene expression of pediatric patients with biophenotypic leukemia.

Keywords: Patient sample accumulation

overall_design: The patient samples were selected from database review, and gene expressions were accumulated for the corresponding study period.

first: Jeffrey

middle: E

last: Rubnitz

first: Mihaela

last: Onciu

first: Stanley

last: Pounds

first: Sheila

last: Shurtleff

first: Susana

middle: C

last: Raimondi

first: Frederick

middle: G

last: Behm

first: Bassem

middle: I

last: Razzouk

first: Raul

last: Ribeiro

first: James

middle: R

last: Downing

first: Ching-Hon

last: Pui


title: Euctopic and ectopic human endometrium (endometriosis)

status: Public on Dec 22 2008

city: Cambridge

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

country: United Kingdom

institute: University of Cambridge

summary:
The pathophysiology of endometriotic lesion development remains unclear but involves a complex interaction between ectopic endometrium and host peritoneal tissues. We hypothesised that disruption of this interaction was likely to suppress endometriotic lesion formation. We hoped to delineate the molecular and cellular dialogue between ectopic human endometrium and peritoneal tissues in nude mice, as a first step towards testing this hypothesis. Human endometrium was xenografted into nude mice and the resulting lesions were analysed using microarrays. A novel technique was developed that unambiguously determined whether RNA transcripts identified by the microarray analyses originated from human cells (endometrium) or mouse cells (stroma).  Four key pathways (ubiquitin/proteosome, inflammation, tissue remodelling/repair and ras-mediated oncogenesis) were revealed, that demonstrated communication between host stromal cells and ectopic endometrium.

Keywords: Disease state analysis

overall_design: Paired samples of eutopic and ectopic endometrium from 9 individual women were collected and the transcript profiles compared.

first: D

middle: S


title: Genome-wide profiling of salt fractions maps physical properties of chromatin

status: Public on Dec 12 2008

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: Genome binding/occupancy profiling by genome tiling array

summary:
We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80mM or 150mM NaCl after digestion contain predominantly mononucleosomes and represent calssical 'active' chromatin. Profiles of these low-salt-soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of RNA polymerase II. Nearly quantitative recovery of chromatin is obtained with 600mM NaCl, however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics.

Keywords: Chromatin affinity-purification on microarray

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and  http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: All experiments were done using two channels per chip, comparing DNAs extracted from either salt-extracted or insoluble chromatin to whole nuclear chromatin, whole nuclear chromatin to randomly fragmented genomic DNA, streptavidin-bound biotin-tagged histone-variant-containing chromatin to salt-extracted chromatin, gel-purified mononucleosomes to whole EDTA-extracted soluble chromatin, streptavidin-bound biotin-tagged histone-variant-containing chromatin to whole EDTA-extracted soluble chromatin, or oligo(dT)-primed cDNA to randomly fragmented genomic DNA from S2 cell nuclei.

first: Steve

first: Kami

last: Ahmad


title: Plant response to misfolded protein in the cytosol

status: Public on Dec 11 2008

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

summary:
Virus infection and over expression of protein in cytosol induce a subset of HSP70s. We named this response the Cytosolic Protein Response (CPR) and have been investigating it in the context of a parallel mechanism in the soluble cytosol with the UPR, and as a subcomponent of the larger HS response. This experiment was carried out to study the transcriptional aspect of CPR. In this analysis, we have triggered CPR by infiltrating proline analogue, L-azetidine-2-carboxylic acid (AZC) into Arabidopsis mature leaves. Since AZC trigger unfolded protein response(UPR) in ER as well as CPR, we have included tunicamycin treatment, which is a specific inducer of UPR to subtract the effect of UPR from the AZC response. Heat shocked samples were included to identify CPR as a subcomponent of larger HS response.
We used microarray data to identify the genes upregurated by CPR. These genes were commonly upregulated by AZC and HS but not by tunicamycin treatment.

Keywords: stress response

overall_design: Arabidopsis mature leaves were infiltrated with AZC or L-Proline (control of AZC) and tunicamycin or DMF(solvent control of tunicamycin). For the heat shock treatment, six mature leaves were detached from plant and incubated at 37 °C or 20°C (as a control) for a period of 1h. The experiment was repeated three times for AZC and HS treatment (3 biological replication). Tunicamycin experiment was repeated five times due to large valiation in the responses (5 biological replication).

first: Akiko

last: Sugio

first: Andrew

last: Maule


title: Gene expression in human myeloid cells.

status: Public on Dec 10 2008

city: Modena

first: Francesco

last: Ferrari

address: Via G. Campi 287

department: Department of Biomedical Sciences

country: Italy

institute: University of Modena and Reggio Emilia

summary:
Human myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where pluripotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. This study aimed at investigating the genomic expression during myeloid differentiation through a computational approach that integrates gene expression profiles with functional information and genome organization. The genomic distribution of myelopoiesis genes was investigated integrating transcriptional and functional characteristics of genes. The analysis of genomic expression during human myelopoiesis using an integrative computational approach allowed discovering important relationships between genomic position, biological function and expression patterns and highlighting chromatin domains, including genes with coordinated expression and lineage-specific functions.

The RMA normalized data, analyzed using Bioconductor packages and RMA pre-processing procedure are available as a supplementary file on the Series record.

overall_design: The gene expression dataset obtained by our laboratory was enriched including third party expression data, from a public repository. Final gene expression dataset includes 24 experiments for 8 different cell types of the human myelopoietic lineage, which were used to generate an integrated myelopoiesis dataset.

first: Sergio


title: D. simulans vs. Sechellia bodies choice vs. no choice -Affymetrix

status: Public on Nov 25 2008

city: East Lansing

first: Ian

last: Dworkin

state: MI

address: 203 Natural Science Bldg. Michigan State University

department: Zoology

institute: Michigan State University

summary:
Here we show that Drosophila sechellia—a specialist on the fruit of Morinda citrifolia that recently diverged from its generalist sister-species, D. simulans—has rapidly accumulated loss-of-function alleles and reduced gene expression at genes affecting olfaction, detoxification, and metabolism.
While D. sechellia increases expression of genes involved with oogenesis and fatty acid metabolism when on its host, many more genes show reduced expression in D. sechellia.  For several functionally related genes, this decrease in expression is associated with loss-of-function alleles.  The rapid accumulation of these alleles potentially affected D. sechellia’s initial adaptation to M. citrifolia, likely contributes to D. sechellia’s poor competitive ability off of its host, and increases ecological isolation between D. sechellia and its sister species.

Keywords: comparative hybridization, gene expression

sample_organism:
Drosophila sechellia
Drosophila simulans

overall_design: 2 species (simulans and sechella) by choice vs no-choice treatment for octanoic & hexanoic acid blend

first: Corbin

last: Jones


title: Downstreams of hnRNP A2 in Colo16 cells

status: Public on Dec 01 2008

city: Brisbane

first: Yaowu

last: He

state: Queensland

address: Cooper Road

department: School of Molecular and Microbial Sciences

country: Australia

institute: University of Queensland

summary: Limited knowledge of the downstream targets of hnRNP A2/B1 has, however, precluded a clear understanding of their roles in cancer cell growth. To define the pathways in which this protein acts we have now carried out microarray experiments with total RNA from Colo16 epithelial cells transfected with an shRNA that markedly suppresses hnRNP A2/B1 expression. The microarray data identified 123 genes, among 22283 human gene probe sets, with altered expression levels in hnRNP A2/B1-depleted cells. Ontological analysis showed that many of these downstream targets are involved in regulation of the cell cycle and cell proliferation and that this group of proteins is significantly over-represented amongst the affected proteins. The changes detected in the microarray experiments were confirmed by real-time PCR for a subset of proliferation-related genes. Immunoprecipitation-RT-PCR demonstrated that hnRNP A2/B1 formed complexes with the transcripts of many of the verified downstream genes, suggesting that hnRNP A2/B1 contributes to the regulation of these genes.

overall_design:
Western blotting was performed to confirm the efficient suppression of hnRNP A2/B1 by shRNA, which was endogenously generated from a pSUPER vector system. A vector carrying a target sequence of firefly was used as a control. The specificity of the hnRNP A2/B1 targeting vector has been established in our previous study [Yaowu He, Melissa A. Brown, Joseph A. Rothnagel, Nicholas A. Saunders, and Ross Smith. Roles of heterogeneous nuclear ribonucleoprotein A/B in cell proliferation. Journal of Cell Science. 2005.118(14):3173-83]

For microarray hybridization, the GeneChip Human Genome U133A platform (Affymetrix) used in this study was printed with 22,283 oligonucleotide probe sets representing 18,400 transcripts and variants, including 14,500 known genes. For a probe set, there were typically 8 probe pairs, each containing a perfect match and a mismatch oligonucleotide. Two chips were prepared for each treatment, allowing 4 comparisons between the hnRNP A2-suppressed and the control cells (samples were not paired).

first: Joseph

middle: A

last: Rothnagel

first: Michael

last: Epis

first: Peter

middle: J

last: Leedman

first: Ross

last: Smith


title: Lung selective gene responses to alveolar hypoxia

status: Public on Nov 21 2008

city: Dublin

first: Christine

middle: Marie

last: Costello

address: University College Dublin

country: Ireland

institute: Conway Institute

summary:
Pulmonary hypoxia is a common complication of chronic lung diseases leading to the development of pulmonary hypertension.  The underlying sustained increase in vascular resistance in hypoxia is a response unique to the lung.  Thus, we hypothesised that there are genes whose expression is altered selectively in the lung in response to alveolar hypoxia.
Using a novel subtractive array strategy, we compared gene responses to hypoxia in primary human pulmonary microvascular endothelial cells to those in cardiac microvascular endothelium and identified genes selectively differentially regulated in the lung endothelium.
Keywords: Time course, cell type comparison

overall_design: Human microvascular endothelial lung (n=3) or cardiac (n=3) cells in normoxia (21% O2), or hypoxia (1% O2) for 3hrs, 24hrs or 48hrs.

middle: M


title: Expression profiling in LGMD2A muscles

status: Public on Nov 18 2008

city: San Sebastian

first: Amets

last: Saenz

state: Gipuzkoa

address: Pº dr Begiristain s/n

country: Spain

institute: Donostia Hospital

summary:
The aim of this study was to identify the genes showing an altered expression in LGMD2A patients and the possible pathways they are implicated in. Ten muscle samples from patients with calpainopathy in which molecular diagnosis was ascertained were invest

Keywords: Comparative genomic hybridization

overall_design: We used 10 microarrays of LGMD2A patients and 10 microarrays of control muscles. EXP-2, EXP-4 and EXP-28 HG-U133B arrays were excluded from the analysis due to problems with the samples.

last: Sáenz


title: Integrin alpha6-beta4 control the expression of genes associated with cell motility, invasion and metastasis

city: Galveston

first: Kathleen

middle: L

last: O' Connor

state: TX

address: 301 University Blvd

department: Surgery

institute: University of Texas Medical Branch

summary:
The objective of this study was to determine the gene expression changes mediated by the alpha6beta4 integrin using MDA-MB-435 breast carcinoma cell line under normal culturing conditions (10% FCS in DMEM).
Keywords: Transfection (stable)

overall_design: Comparison of clones of MDA-MB-435 cells transfected with the integrin beta4 subunit (which results in cell surface expression of the integrin apha6beta4 integrin; clones 3A7 and 5B3) to those transfected with vector (mock; 6D2 and 6D7) only.

first: Min

last: Chen

first: Mala

last: Sinha

last: O'Connor


title: Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours

status: Public on Dec 24 2008

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

summary: Inflammatory hepatocellular adenomas (IHCA) are benign liver tumours defined by the presence of inflammatory infiltrates and by the elevated expression of inflammatory proteins in tumour hepatocytes1,2. Here we show a striking activation of the IL6 signalling pathway in this tumour type, and sequencing candidate genes pinpointed this response to somatic gain-of-function mutations in the IL6ST gene that encodes the signalling co-receptor gp130. Indeed, ~70% of IHCA harbour small in-frame deletions that target the binding site of gp130 for IL6, and expression of the most frequent gp130 mutant, Delta-STVY190, in hepatocellular cells activates STAT3 in absence of ligand. Further, analysis of hepatocellular carcinomas revealed rare gp130 alterations always accompanied by ß-catenin-activating mutations, suggesting a cooperative effect of these signalling pathways in the malignant conversion of hepatocytes. The recurrent gain-of-function gp130 mutations in these human hepatocellular adenomas explains their inflammatory phenotype, and suggest that similar alterations may occur in other inflammatory epithelial tumours with STAT3 activation.

overall_design: HG-U133A Affymetrix GeneChipTM arrays were used to compare the expression profiles of 4 Inflammatory hepatocellular adenomas (IHCA) and 4 non related non-tumor livers. RNA labelling, hybridization and analysis were carried out following the manufacturer’s instructions (Affymetrix, Santa Clara, CA). Raw data were obtained by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Santa Clara, USA); the resulting raw numerical data (CEL files) - available as supplementary files - collected from 8 Affymetrix GeneChips were pre-processed for normalization and filtering as described in [Rebouissou et al., J Biol Chem 2007, 282(19):14437-46, PMID: 17379603; Rebuissou et al., J Hepatol 2008, 49(1):61-71. PMID: 18466996 and Rebuissou et al., in preparation].

first: Sandra

last: Rebuissou

first: Mohamed

last: Amessou

first: Gabrielle

last: Couchy

first: Tina

last: Izard

first: Charles

last: Balabaud

first: Paulette

last: Bioulac-Sage

first: Jessica

last: Zucman-Rossi


title: Studying Gene Expression Profiles of UV-Irradiated Human Keratinocytes by cDNA Microarray

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

summary:
The goal of this thesis is to study the response of a human keratinocyte cell line (HaCaT cells) after UVB irradiation. In order to develop a system for UV irradiation, we firtstly studied the UV illumination system to find out a stable and reliable condition for UV irradiation experiments. Further, we found out the proper dose of UVB radiation and time points after UVB irradiation by performing MTT assay and trypan blue viability test. According to the results of MTT assay and trypan blue viability test, the cellular activity as well as survival rate of UVB-irradiated cells were in proportion to the radiation doses within a lower UVB dose range. We wanted to find out the possible reasons for this phenomenon by using cDNA microarray. We hope the thesis could be a guide for the following researches, and be useful in the clinical studies about the UV damage.
Keywords: dose response and time course

overall_design: Loop-designed microarray experiments were performed in our study. Twenty-one samples are arranges as seven small loops and one large loop, with three and seven microarray slides for each small and large loop, respectively. This set of loop-designed microarray experiment contains one control untreated (non UVB-treated) samples and two UVB-treated samples (one low dose and one high dose UVB-treated) at each time point (total seven time points).

first: Chiu-Ting

first: Ching-Lung

last: Huang


title: The zinc finger protein Zelda plays a key role in the maternal to zygotic transition in Drosophila

status: Public on Nov 17 2008

city: New York

last: Rushlow

state: NY

address: 100 Washington Sq.E.

department: Biology

institute: NYU

summary:
In all animals, the initial events of embryogenesis are controlled by maternal gene products that are deposited into the developing oocyte. At some point after fertilization, control of embryogenesis is transferred to the zygotic genome in a process called the maternal to zygotic transition (MZT). During this time maternal RNAs are degraded and zygotic RNAs are transcribed1. A long standing question has been, what factors regulate these events? The recent findings that microRNAs and Smaugs mediate maternal transcript degradation brought new life to this old problem2,3, however, the transcription factors that activate zygotic gene expression remained elusive. A clue came from the finding that many early zygotic genes in Drosophila share a cis-regulatory heptamer motif, CAGGTAG and related sequences, collectively referred to as TAG-team sites4,5. We asked whether there was a dedicated transcription factor that interacts with these sites to activate early genes. Here we report the discovery of a zinc-finger protein, Zelda (Zld) that binds specifically to TAG-team sites, and is capable of activating transcription in transient transfection assays. Mutant embryos lacking zld are defective in the cellularization process, and fail to activate the transcription of many early zygotic genes involved in cellularization, sex determination, and dorsoventral patterning. Global expression profiling confirmed that Zld plays a key role in the activation of the early zygotic genome, and suggests that Zld may also play a role in maternal RNA degradation during the MZT since many RNAs are up-regulated in the absence of Zld.
Keywords: Drosophila early embryo, MZT, transcriptional activator

overall_design: Total RNA samples were extracted from three replicate collections of 1-2 hr yw and M- zld embryos by TRIzol (invitrogen). A portion of the collected embryos was fixed and stained with DAPI; 90% were in nuclear cycles 8 to13. cDNA was prepared using the GeneChip® HT One-Cycle cDNA Synthesis Kit (Manufactured by Invitrogen for Affymetrix) and labeled with the BioArray™ HighYield™ RNA Transcript Labeling Kit (Enzo). Labeled probes were hybridized to Drosophila Genome 2 Affymetrix arrays and processed by a GeneChip Fluidics Station 400. Data were acquired and normalized by the GeneChip® Scanner 3000 and processed by the Affymetrix GeneChip Operating Software (GCOS). t-test analysis was performed on the data from three biological replicates.

first: Chung-Yi

last: Nien

first: Hsiao-Lan

last: Liang

first: Hsiao-Yun

last: Liu

first: Mark

last: Metzstein

first: Nikolai

last: Kirov


title: 25-hydroxycholesterol effects on human hepatocyte metabolism and the antiviral state it conveys against the HCV

status: Public on Dec 25 2008

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

summary:
Hepatitis C virus (HCV) infection is a global health problem. A number of studies have implicated a direct role of cellular lipid metabolism in the HCV life cycle and inhibitors of the mevalonate pathway have been demonstrated to result in an antiviral state within the host cell. Transcriptome profiling was also conducted on Huh-7 human hepatoma cells bearing subgenomic HCV replicons with and without treatment with 25-hydroxycholesterol (25-HC), an inhibitor of the mevalonate pathway that alters lipid metabolism, to assess metabolic determinants of pro- and antiviral states within the host cell.

Keywords: treatment and time course

overall_design: compound treatment and time course

last: Walker

first: Selena

last: Sagan

first: Andrew

last: Su

first: Lubica

last: Supekova

first: Yanouchka

last: Rouleau

first: Angela

last: Tonary


title: Molecular and transcriptional characterization of chromosome 17p loss in chronic lymphocytic leukemia

status: Public on Nov 11 2008

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

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

summary:
Distinct genetic abnormalities such as TP53 deletion at 17p13.1, have been identified as having an adverse prognostic relevance in B-cell chronic lymphocytic leukemia (B-CLL). Conventional cytogenetic studies have shown that TP53 deletion in B-CLL is associated predominantly with 17p loss resulting from complex chromosomal rearrangements. We performed genome-wide DNA (SNPs arrays), fluorescence in situ hybridization (FISH) and gene expression profiling (GEP) analyses to investigate the significance of 17p loss in a panel of 71 genetically well-characterized B-CLLs in Binet stage A, 18 of which carried a TP53 monoallelic deletion. Combined SNP arrays and FISH approaches showed 17p loss in all of the TP53-deleted cases, with breakpoints scattered along the 17p11.2 region. Mutations in exons 5 to 9 of TP53 were found in 9/12 deleted samples. GEP of 60 B-CLLs, including 7 patients with 17p loss, identified 40 differentially expressed genes in 17p- versus 17p normal samples, 35 of which were down-regulated in 17p- tumors. The majority (30/35) of these transcripts, including putative tumor suppressor genes, mapped to 17p. Overall, these data indicate that, beside TP53 deletion, the concomitant loss of 17p arm may contribute to the strong negative prognostic impact known to be associated with this lesion in B-CLL.

This SuperSeries is composed of the SubSeries listed below.


title: Expression data from LNCaP cells transfected with SOX4 cDNA, SOX4 siRNA or GFP cDNA

status: Public on Nov 10 2008

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary:
SOX4 is a critical developmental transcription factor in vertebrates and is required for   precise differentiation and proliferation in multiple tissues.  In addition, SOX4 is   overexpressed in many human malignancies, but the precise role of SOX4 in cancer   progression is not well understood.  Here we have either eliminated SOX4 using siRNA or overexpressed a SOX4 cDNA and compared the gene expression patterns against control GFP transfections to identify SOX4 target genes.
Data described in manuscript P. Liu et al., Cancer Res 46, 4011 (April 15, 2006)

Keywords: Gene Expression

overall_design: LNCaP prostate cancer cells were transfected with either a SOX4 cDNA, a pool of SOX4 siRNAs or a control GFP expression vector.  Each transfection was performed in duplicate on two separate days.  Total RNA was harvested 24 hours post-transfection

first: Carlos

last: Moreno

first: Christopher


title: Expression data from human PBMC samples exposed to IL-12 and paired controls

status: Public on Nov 14 2008

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

summary:
The cytokine interleukin-12 (IL-12) is known to play a central role in adaptive and innate immunity.
We employed microarray analysis of IL-12 induced gene expression to provide further insights into its effects on immune response.

Keywords: Paired study of expression levels: Treated vs. Control

overall_design: PBMC's were isolated from 7 healthy NIH blood bank donors.  For each donor, expression levels were measured for PBMCs stimulated with IL-12 and for unstimulated controls, using the Affymetrix Human Genome HG-U133A and HG-U133B GeneChips.

first: Wendy

middle: T

last: Watford

first: Bruce

middle: D

last: Hissong

first: Lydia

last: Durant

first: Hidehiro

last: Yamane

first: Linda

last: Muul

first: Yuka

last: Kanno

first: Cristina

last: Tato

first: Haydee

last: Ramos

first: Lisa

last: Mielke

first: Marko

last: Pesu

first: Benjamin

last: Solomon

first: David

last: Frucht

first: William

last: Paul

last: Sher

first: Dragana

last: Jankovic

first: Philip

middle: N

last: Tsichlis

last: O’Shea


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis

status: Public on Nov 08 2008

city: Palmerston North

first: Mingshu

last: Cao

address: Tennent Drive

country: New Zealand

institute: HortResearch/AgResearch

summary: Examine global gene expression patterns in control and 35S:PAP1 Arabidopsis plants upon environmental perturbation (light and temperature) over the course of the experiments.

overall_design: Red coloured 35S:PAP1, and empty vector control, plants of Arabidopsis thaliana Columbia were grown under room temperature, high light (RTHL, 22°C, 440 µmol m-2 s-1 irradiance) conditions to promote red leaf colouration. The growth conditions were then changed to a high day temperature, low light (HTLL: 30°C day, 150 µmol m-2 s-1 irradiance) stress treatment for six days, during which time the 35S:PAP1 leaves lost much of their red colouration, turning green.  The growth conditions were then returned to a low temperature high light (LTHL, 15°C, 62% RH, 440 µmol m-2 s-1 irradiance) regime to restore the red colouration.

first: Daryl

last: Rowan

first: Andrew

last: Allan

first: Kui

last: Lin-Wang

first: Robert

last: Schaffer

first: Roger

middle: P

last: Hellens

first: Martin

middle: B

last: Hunt

first: Paul

last: Austin

first: Cara

last: Norling

first: Dwayne

last: Jensen

first: Janine

last: Cooney


title: Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass

status: Public on Nov 07 2008

city: Maastricht

first: Arie

last: van Erk

address: UNS 40

country: Netherlands

institute: BiGCaT Bioinformatics

summary: Left ventricular mass (LVM) and cardiac gene expression are complex traits regulated by factors both intrinsic and extrinsic to the heart. To dissect the major determinants of LVM, we combined expression quantitative trait locus1 and quantitative trait transcript (QTT) analyses of the cardiac transcriptome in the rat. Using these methods and in vitro functional assays, we identified osteoglycin (Ogn) as a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM. We also applied genome-wide QTT analysis to the human heart and observed that, out of 22,000 transcripts, OGN transcript abundance had the highest correlation with LVM. We further confirmed a role for Ogn in the in vivo regulation of LVM in Ogn knockout mice. Taken together, these data implicate Ogn as a key regulator of LVM in rats, mice and humans, and suggest that Ogn modifies the hypertrophic response to extrinsic factors such as hypertension and aortic stenosis.

overall_design: 7 cardiac biopsies from control patients and 20 cardiac biopsies from aortic stenosis patients

first: Blanche

last: Schroen

first: Yigal

last: Pinto


title: Effects of glucocorticoids and Protein Kinase A on growth factor- and  1beta- regulated gene

status: Public on Nov 01 2008

city: Winston-Salem

first: Anna

last: Misior

state: NC

address: Medical Center Blvd

department: Center for Human Genomics

institute: Wake Forest University

summary:
Glucocorticoids (GCs) and protein kinase A (PKA)-activating agents (beta-adrenergic receptor agonists) are mainstream asthma therapies based on their ability to prevent or reverse excessive airway smooth muscle (ASM) constriction.  Their abilities to regulate another important feature of asthma - excessive ASM growth are poorly understood.  Recent studies have suggested that GCs render agents of inflammation such as interleukin 1beta and tumor necrosis factor alpha mitogenic to ASM, via suppression of (antimitogenic) induced cyclooxygenase-2-dependent PKA activity.  To further explore the mechanistic basis of these observations, we assessed the effects of epidermal growth factor and interleukin 1beta stimulation, and the modulatory effects of GC treatment and PKA inhibition, on the ASM transcriptome by microarray analysis.

Keywords: gene expression

overall_design: Human ASM cultures were generated from trachea of 4 unidentified donors and used in passage 5-8.  These cells were used to generate cells stabely expressing a PKA inhibitor (PKI) or GFP (control), which were then grown to confluence, serum starved for 24h, and stimulated with IL-1b,  EGF,or both (E+I) in presence or absence of Fluticasone (Flu, 30 min pretreatment). After 8h stimulation cells were washed and total RNA isolated using TRIzol as per manufacturer's protocol.  Gene expression was analyzed in 4 different cultures derived from 4 different donors (for a total of 3-4 microarrays per condition).

first: Raymond

last: Penn


title: Crosstalk between Estrogen and TNFalpha in MCF-7 Breast Cancer Cells

city: Chicago

first: Jonna

last: Frasor

state: IL

address: 835 S. Wolcott MC 901

institute: University of Illinois at Chicago

summary:
Study was carried out to examine how E2 and TNFa together influence gene expression in breast cancer cells compared to either factor alone.
Keywords: drug response

overall_design: MCF-7 cells were treated with 10 nM E2, 10 ng/ml TNFa, or both for 2h. Experiment was carried out in triplicate.


title: A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks

city: Davis

first: Wei

last: Hu

state: CA

address: One Shields Ave.

department: Department of Molecular and Cellular Biology

institute: Univ of California at Davis

summary: Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer light-independent, constitutive photomorphogenic (cop) phenotypes to transgenic plants (Su & Lagarias 2007 Plant Cell 19, 2124-2139). In the present study, comparative transcript profiling experiments were performed to assess whether the pattern of gene expression regulated by these alleles accurately reflects the process of photomorphogenesis in wild-type Arabidopsis. Whole genome transcriptional profiles of dark-grown phyAphyB seedlings expressing the Y276H mutant of phyB (YHB) revealed that YHB reprograms about 13% of the Arabidopsis transcriptome in a light-independent manner. The YHB-regulated transcriptome proved qualitatively similar to, but quantitatively greater than those of wild-type seedlings grown under 15 or 50 umol m-2 m-1 continuous red light (Rc). Among the 2977 genes statistically significant two-fold (SSTF) regulated by YHB in the absence of light include those encoding components of the photosynthetic apparatus, tetrapyrrole/pigment biosynthetic pathways and early light-responsive signaling factors. Approximately 80% of genes SSTF regulated by Rc were also YHB-modulated. Expression of a notable subset of 346 YHB-regulated genes proved to be strongly attenuated by Rc, indicating compensating regulation by phyC-E and/or other Rc-dependent processes. Since the majority of these 346 genes are regulated by the circadian clock, these results suggest that phyA- and phyB-independent light signaling pathway(s) strongly influence clock output. Together with the unique plastid morphology of dark-grown YHB seedlings, these analyses indicate that the YHB mutant induces constitutive photomorphogenesis via faithful reconstruction of phyB signaling pathways in a light-independent fashion.

overall_design:
16 samples: 9 are dark-grown samples (3 samples x 3 replicates), 6 are continuous red light (Rc)-grown samples (3 samples x 2 replicates).

wild type grown in darkness, three independent biological replicates;
phyA-201phyB-5 mutant grown in darkness, three independent biological replicates;
YHB (AtPHYB-YH/phyA-201phyB-5) grown in darkness, two independent transgenic lines, three independent biological replicates;
wild type grown under 15 umol m-2 s-1 Rc, two independent biological replicates;
wild type grown under 50 umol m-2 s-1 Rc, two independent biological replicates;
YHB (AtPHYB-YH/phyA-201phyB-5) grown under 50 umol m-2 s-1 Rc, one transgenic line used, two independent biological replicates

first: Clark

last: Lagarias


title: ERRγ mediates Tamoxifen resistance in novel models of invasive lobular breast cancer

city: Washington

first: Rebecca

middle: B.

last: Riggins

state: DC

address: E412 Research Building, 3970 Reservoir Rd. NW

department: Oncology, and Lombardi Comprehensive Cancer Center

institute: Georgetown University

summary: One-third of all ER+ breast tumors treated with endocrine therapy fail to respond, and the remainder are likely to relapse in the future.  Almost all data on endocrine resistance has been obtained in models of invasive ductal carcinoma (IDC). However, invasive lobular carcinomas (ILC) comprise up to 15% of newly diagnosed invasive breast cancers diagnosed each year and, while the incidence of IDC has remained relatively constant during the last 20 years, the prevalence of ILC continues to increase among postmenopausal women.  We report a new model of Tamoxifen (TAM)-resistant invasive lobular breast carcinoma cells that provides novel insights into the molecular mechanisms of endocrine resistance.  SUM44 cells express ER and are sensitive to the growth inhibitory effects of antiestrogens.  Selection for resistance to 4-hydroxytamoxifen led to the development of the SUM44/LCCTam cell line, which exhibits decreased expression of estrogen receptor alpha (ERα) and increased expression of the estrogen-related receptor gamma (ERRγ).  Knockdown of ERRγ in SUM44/LCCTam cells by siRNA restores TAM sensitivity, and overexpression of ERRγ blocks the growth-inhibitory effects of TAM in SUM44 and MDA-MB-134 VI lobular breast cancer cells.  ERRγ-driven transcription is also increased in SUM44/LCCTam, and inhibition of activator protein 1 (AP1) can restore or enhance TAM sensitivity.  These data support a role for ERRγ/AP1 signaling in the development of TAM resistance, and suggest that expression of ERRγ may be a marker of poor Tamoxifen response.

overall_design: Total RNA was extracted from sub-confluent T-25 cm^2 tissue culture flasks of SUM44 and LCCTam cells, then processed and arrayed.  Microarray data quality was then assessed using several tools, including those recommended by Affymetrix and a series of additional QC measures. The Robust Multiple-Array Average (RMA) method was used to preprocess the raw gene expression data, as implemented in the Bioconductor project (http://bioconductor.org). We then isolated a reduced dimension dataset that included genes that exhibit ≥2 fold change, p<0.05 and genes with intensity ≥log2(10) in both SUM44 and SUM44/LCCTam groups.  Data visualization before and after dimensionality reduction was facilitated by multidimensional scaling as estimated using Principal Component Analysis (PCA) and Discriminant Component Analysis (DCA), to ensure that the global structure of the data was not altered by dimensionality reduction procedures.

first: Jennifer

last: Lan

first: Yuelin

last: Zhu

first: Uwe

last: Klimach

first: Alan

last: Zwart

first: Luciane

last: Cavalli

first: Bassem

last: Haddad

first: Li

last: Chen

first: Ting

last: Gong

first: Jianhua

last: Xuan

first: Stephen

last: Ethier

last: Clarke


title: Prostate cancer cell lines and normal prostate epithelial and stromal cells in primary culture

first: Srinivasan

last: Yegnasubramanian

address: 1650 Orleans Street, CRB1 Rm 1M53

summary: The primary goal of this study was to assess differences in gene expression between prostate cancer cell lines and normal prostate epithelial and stromal cells in primary culture.

overall_design: 9 samples were analyzed with 1 replicate each. Samples included 6 prostate cancer cell lines, 1 normal prostate epithelial cell system in primary culture, and 2 normal prostate stromal cell systems in primary culture.

first: William

middle: G

last: Nelson


title: Gene expression analysis of HESC derived teratomas

city: Jerusalem

first: Nissim

last: Benvenisty

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

summary: Gene expression analysis of human embryonic stem cell derived tumors (teratomas).

overall_design: Undifferentiated HESCs were injected into the testis or under the kidney capsule of SCID-NOD mice and were let to grow for one month prior to tumor harvesting.

first: Barak

last: Blum

first: Ofra

last: Yanuka

first: Micha

last: Drukker

first: Yoav

last: Mayshar


title: Aging hematopoietic progenitor/stem cells

city: Seattle

first: Derek

last: Stirewalt

address: 1100 Fairview Ave N, D5-112

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: To determine how aging impacts gene expression in hematopoietic stem cells (HSCs), human CD34+ cells from bone marrow (34BM) and mobilized stem cell products (34P38NPBSC) were examined using microarray-based expression profiling. Differential expression changes were confirmed by microarray comparisons of younger and older expanded T-cell populations.

overall_design: We compared gene expression profiles between younger and older human CD34+ cells from bone marrow (34BM) and CD34+CD38- cells from mobilized stem cell products(34P38NPBSC). We also examined gene expression changes associated with aging in human expanded T-cells. For 34BM and T-cells, biotin-labeling of total RNA (5 µg) was performed as per standard Affymetrix protocol.  For the 34P38NPBSC arrays, the single-stranded linear amplification protocol was used to process total RNA (100 nanograms) for the microarrays.  Both protocols are described in detail in PMID14706461.

first: Yongjae

middle: E

last: Choi

first: Norman

last: Sharpless

first: Era

last: Pogosova-Agadjanyan

first: Michelle

last: Cronk

first: Michi

last: Yukawa

first: Eric

last: Larson

first: Brent

last: Wood

first: Frederick

last: Appelbaum

first: Jerald

last: Radich

first: Shelly

last: Heimfeld


title: Gene expression patterns in peripheral blood correlate with the extent of coronary artery disease

status: Public on Oct 31 2008

city: Basel

first: Peter

last: Grass

address: Klybeck Strasse

department: DMP

institute: Novartis

summary:
Gene expression profile in circulating leukocytes identifies patients with coronary artery disease

Peter Sinnaeve, Mark Donahue, Peter Grass, Jacky Vonderscher, David Seo, Pascal Goldschmidt, Christopher Granger

Department of Medicine, Duke University, Durham, NC, USA, Novartis Institute for Biomedical Research, Cambridge, Boston, MA, USA

Introduction

Systemic and local inflammation plays a prominent pathogenetic role in atherosclerotic coronary artery disease (CAD), but the relationship of phenotypic changes in circulating leukocytes and extent of CAD remains unclear. We have investigated whether gene expression patterns in circulating leukocytes are associated with presence and extent of CAD.

Methods

Patients undergoing coronary angiography were selected according to their Duke CAD index (CADi), a validated angiographical measure of the extent of coronary atherosclerosis that correlates with outcome. RNA was extracted from 110 patients with CAD (CADi>23) and from 112 partially matched controls without CAD (CADi=0). Gene expression was assessed using Affymetrix U133A chips. Genes correlating with CAD were identified using Spearman’s rank correlation, and predictive gene expression patterns were identified using a partial least squares (PLS) regression analysis.

Results

160 individual genes were found to significantly correlate with CADi (rho>0.2, P<0.0027), although changes in individual gene expression were relatively small (1.2 to 1.5 fold). Using these 160 genes, the PLS multivariate regression resulted in a highly predictive model (r2=0.764, P<0.001). Cross-validation showed that most of the predictive model was carried by only 8 genes (r2=0.752) (table 1).

Conclusion

Simultaneous expression pattern of 8 genes appears to be highly predictive for CAD. Peripheral leukocyte gene expression pattern could be a novel non-invasive biomarker for CAD and lead to new pathophysiologic insights.

overall_design: parallel group design

last: Sinnaeve


title: Microarray analysis of MINI ZINC FINGER 1 (MIF1) overexpression transgenic Arabidopsis seedlings

first: Wei

last: Hu

summary: Phytohormones play crucial roles in regulating many aspects of plant development. Although much has been learned about the effects of individual hormones, cross-talk between and integration of different hormonal signals are still not well understood. We present a study of MINI ZINC FINGER 1 (MIF1), a putative zinc finger protein from Arabidopsis, and suggest that it may be involved in integrating signals from multiple hormones. MIF1 homologs are highly conserved among seed plants, each characterized by a very short sequence containing a central putative zinc finger domain. Constitutive overexpression of MIF1 caused dramatic developmental defects, including dwarfism, reduced apical dominance, extreme longevity, dark-green leaves, altered flower morphology, poor fertility, reduced hypocotyl length, spoon-like cotyledons, reduced root growth, and ectopic root hairs on hypocotyls and cotyledons. In addition, 35S::MIF1 seedlings underwent constitutive photomorphogenesis in the dark, with root growth similar to that in the light. Furthermore, 35S::MIF1 seedlings were demonstrated to be non-responsive to gibberellin (GA) for cell elongation, hypersensitive to the GA synthesis inhibitor paclobutrazol (PAC) and abscisic acid (ABA), and hyposensitive to auxin, brassinosteroid and cytokinin, but normally responsive to ethylene. The de-etiolation defect could not be rescued by the hormones tested. Consistent with these observations, genome-scale expression profiling revealed that 35S::MIF1 seedlings exhibited decreased expression of genes involved in GA, auxin and brassinosteroid signaling as well as cell elongation/expansion, and increased expression of ABA-responsive genes. We propose that MIF1, or the protein(s) with which MIF1 interacts, is involved in mediating the control of plant development by multiple hormones.

overall_design: The experiment was designed to compared expression profiles of wild type (vector transformed Col) and 35S::MIF1 seedlings grown in the dark or white light. Twelve affymetrix ATH1 arrays were used for three biological replicates, six for comparison of light-grown seedlings and the other six for dark-grown seedlings. Wild-type seedlings were from three independent vector transformant lines(#1, #4 and #7). For the 35S::MIF1 transgenic seedlings, MIF1OE#124 was used for the first and second replicates, and MIF1OE#127 was used for the third replicate.

first: Hong

last: Ma


title: Gene expression analysis of pre-defined sets of neoplastic tissues

status: Public on Nov 19 2008

city: Torino

first: Daniela

last: Cimino

state: Torino

address: Via Nizza 52

department: Oncological Science

institute: Molecular Biotechnology Center

summary:
To identify a group of genes, characteristic of a single neoplasia and determinant for the risk to relapse, we have performed gene expression analysis of ductal breast carcinoma samples using Affymetrix oligonucletide microarray (HU133A).
Biopses from 60 patients, 30 good prognosis (desease free from six to ten years after surgical treatment) and 30 poor prognosis, have been analyzed. From each group we have created six homogeneous pools to show, during the analysis, only genes expressed in a greatly different way. A reduced number of cases has been used to avoid dilution of genes expressed only in few samples.
Analysis have identified 77 candidate genes with a specific ontological distribution that contained some genes that were linked to breast cancer by previous studies.
Microarray results validation has been performed by real-time PCR analysis on  127 single cases of breast cancer.
Gene function study and literature data allow to define our candidate genes as potential markers of prognosis.
Keywords: Breast cancer gene expression analysis

overall_design: From a group of 130 frozen tumor samples, 30 cases of ductal invasive carcinoma with recurrence within 72 months from surgery (high-risk) and 30 without recurrence (low-risk) were selected for microarray analysis. From each group, 6 RNA pools of 5 samples each were prepared and analyzed on GeneChip Human Genome U133A oligonucleotide microarrays. Hybridizations were performed in technical duplicates, in two experimental sessions.

first: Luca

last: Fuso

first: Christian

last: Sfiligoi

first: Nicoletta

last: Biglia

first: Rccardo

last: Ponzone

first: Furio

last: Maggiorotto

first: Giandomentico

last: Russo

first: Luigi

last: Cicatiello

first: Alessandro

last: Weisz

last: Taverna

first: Piero

last: Sismondi

first: Michele

last: De Bortoli


title: Gene expression analysis of paediatric acute lymphoblastic leukaemia

status: Public on Oct 23 2008

city: Birmingham

first: Carmel

last: McConville

state: UK

address: Vincent Drive

department: School of Cancer Sciences

institute: University of Birmingham

summary:
We addressed the clinical significance and mechanisms behind in vitro cellular responses to ionising radiation (IR)-induced DNA double strand breaks in 74 paediatric ALL patients. We found an apoptosis-resistant response in 36% of patients and an apoptosis-sensitive response in the remaining 64% of leukaemias. Global gene expression profiling of 11 apoptosis-resistant and 11 apoptosis-sensitive ALLs revealed abnormal up-regulation of multiple pro-survival pathways in response to IR in apoptosis-resistant leukaemias and differential post-transcriptional activation of the PI3-Akt pathway was observed in representative resistant cases. It is possible that abnormal pro-survival responses to DNA damage provide one of the mechanisms of primary resistance in ALL .

Keywords: Gene expression profiling; response to irradiation

overall_design: Twenty two B-precursor ALL tumours (11 responsive to IR-induced DNA damage and 11 resistant) were analysed before and 8 hours after exposure to 5 Gy IR, using the Affymetrix HG_U133A (GPL96) platform.

first: Tanja

last: Stankovic

first: Eliot

last: Marston

first: Francesco

last: Falciani


title: Heterogeneous in vitro effects of doxorubicin on gene expression in primary human liposarcoma cultures

status: Public on Oct 06 2008

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

summary:
Doxorubicin is considered one of the most potent established chemotherapeutics in the treatment of liposarcoma; however, the response rates usually below 30%, are still disappointing. This study was performed to identify gene expression changes in liposarcoma after doxorubicin treatment. Cells of 19 primary human liposarcoma were harvested intraoperatively and brought into cell culture. Cells were incubated with doxorubicin for 24 h, RNA was isolated and differential gene expression was analysed by the microarray technique.
We used microarrays to detail the global  gene expression changes following doxorubicin treatment of primary liposarcoma cell cultures

Keywords: response to chemotherapeutic agent

overall_design: We compared untreated primary cell cultures obtained from liposarcoma treated with doxorubicin treated cultures to determine global gene expression changes by microarray analysis

first: L

first: A

last: Daigeler


title: LWD1 and LWD2 in Arabidopsis photoperiod regulation

status: Public on Oct 08 2008

city: Taipei

first: Shu-Hsing

last: Wu

address: 128, Sec 2, Academia Road

institute: Institute of Plant and Microbial Biology, Academia Sinica

summary: Transcriptome analysis has revealed a light-regulated WD (tryptophan and aspartate)-containing protein, LWD1. LWD1 and LWD2 share greater than 90% amino acid sequence homology. The lack of phenotype changes in the lwd1 or lwd2 single mutant implies that the proteins function redundantly. The lwd1lwd2 double mutant, however, has an early flowering phenotype under both long-day (LD) and short-day (SD) conditions. Functional complementation experiment revealed that LWDs are indeed responsible for the defect in photoperiod sensing in lwd1lwd2 double mutant plants. The expression of LWD1 exhibits a diurnal pattern and peaks before dawn. The period length of oscillator (CCA1, LHY, TOC1 and ELF4) and output (CCR2 and CAB2) genes in the lwd1lwd2 double mutant is significantly shorter than that in wild-type Arabidopsis under free running condition. Under entrainment conditions, the expression phase of oscillator (CCA1, LHY, TOC1 and ELF4) and output (GI, FKF1, CDF1, CO and FT) genes shifts ~3 hr forward in the lwd1lwd2 double mutant. Our data indicated that the early flowering phenotype in lwd1lwd2 plants is contributed by the significant phase shift of CO and, therefore, an increased expression of FT before dusk under SD conditions. Our data imply that LWD1/LWD2 proteins function in close proximity to the circadian oscillators for the regulation of photoperiod sensing.

overall_design: Two biological replicates were performed to examine the differential gene expression between wild-type and lwd1lwd2 double mutant. The plants were grown under 12 h L/ 12 h D for 31 days before harvesting their above ground tissues at ZT5-9.

first: Jing-Fen

first: Ying

last: Wang


title: Molecular and transcriptional characterization of chromosome 17p loss in chronic lymphocytic leukemia, experiment A

first: Luca

last: Agnelli

address: Venezian 1

summary:
Distinct genetic abnormalities such as TP53 deletion at 17p13.1, have been identified as having an adverse prognostic relevance in B-cell chronic lymphocytic leukemia (B-CLL). Conventional cytogenetic studies have shown that TP53 deletion in B-CLL is associated predominantly with 17p loss resulting from complex chromosomal rearrangements. We performed genome-wide DNA (SNPs arrays), fluorescence in situ hybridization (FISH) and gene expression profiling (GEP) analyses to investigate the significance of 17p loss in a panel of 71 genetically well-characterized B-CLLs in Binet stage A, 18 of which carried a TP53 monoallelic deletion. Combined SNP arrays and FISH approaches showed 17p loss in all of the TP53-deleted cases, with breakpoints scattered along the 17p11.2 region. Mutations in exons 5 to 9 of TP53 were found in 9/12 deleted samples. GEP of 60 B-CLLs, including 7 patients with 17p loss, identified 40 differentially expressed genes in 17p- versus 17p normal samples, 35 of which were down-regulated in 17p- tumors. The majority (30/35) of these transcripts, including putative tumor suppressor genes, mapped to 17p. Overall, these data indicate that, beside TP53 deletion, the concomitant loss of 17p arm may contribute to the strong negative prognostic impact known to be associated with this lesion in B-CLL.
Keywords: transcriptional analysis of B-CLL with 17p loss patients

overall_design: This series of microarray experiments contains the gene expression profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 60 newly diagnosed patients (Binet stage A). Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome. If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody treatment followed by magnetic beads. 3 micrograms of total RNA was processed and, in accordance with the manufacturer's protocols, 15 micrograms of fragmented biotin-labelled cRNA were hybridized on GeneChip Human Genome U133A Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4) and the probe level data converted to expression values using the Bioconductor function for the Robust Multi-Array average (RMA) procedure (Irizarry et al, 2003), in which perfect match intensities are background adjusted and quantile-quantile normalised.

first: Sonia

last: Fabris

first: Laura

last: Mosca

first: Katia

last: Todoerti

first: Giovanna

last: Cutrona

first: Marta

last: Lionetti

first: Daniela

last: Intini

first: Serena

last: Matis

first: Monica

last: Colombo

first: Massimo

last: Gentile

first: Gianluca

last: Festini

first: Vincenzo

last: Callea

last: Spriano

first: Stefano

last: Molica

first: Giorgio

last: Lambertenghi-Deliliers

first: Fortunato

last: Morabito

first: Manlio

last: Ferrarini

first: Antonino

last: Neri


title: The 76-gene Signature Defines High-Risk Patients that Benefit from Adjuvant Tamoxifen Therapy

status: Public on Oct 07 2008

city: San Diego

first: Jack

last: Yu

address: 3210 Merryfield Row

institute: Veridex, LLC

summary: Classification of tamixifen-treated breast cancer patients into high and low risk groups using the 76-gene signature

overall_design: 136 breast cancer samples that were treated with tamoxifen were classified using the 76-gene signature

first: Yi

last: Zhang

first: Yixin

last: Wang

first: John

last: Fokens


title: Gene expression analysis of Arabidopsis pvip1 pvip2 seedlings

status: Public on Oct 01 2008

city: Lausanne

first: Rene

last: Dreos

address: Ecublens

department: CIG

institute: UNIL

summary:
Early establishment of the apical-basal axis is prerequesite for correct embryonic development in Arabidopsis. The hypophysis is derived from the basal cell of the early embryo and is indispensible for root development; it gives rise to the root quiescent center and the central columella. Arabidopsis pvip1 pvip2 mutants show defects in embryonic root development and give rise to rootless seedlings.
We used microarrays to study the gene regulation of rootless mutant embryos in comparison with wild type.
Keywords: Mutant comparison

overall_design: Arabidopsis pvip1 pvip2 mutant and Col-0 wild type seedlings (10 days after germination) were compared using Affymetrix ATH1 arrays. Roots of wild type seedlings were removed and the vestigial hypocotyl of mutants was cut to control for wounding effects.

first: A

last: Maule

first: D

last: Schmidt

first: R


title: Barrett's vs Normal esophagus vs small intestine comparison

city: Philadelphia

first: Anil

middle: K

last: Rustgi

state: PA

address: 415 Curie Blvd, 600 CRB

department: Medicine-Gastroenterology

institute: University of Pennsylvania

summary:
To begin to identify genes involved in the transdifferentiation process we analyzed Barrett’s esophagus (with no dysplasia), normal esophagus and small intestine biopsy samples by Affymetrix microarray.

Keywords: microarray expression analysis

overall_design: 19 total samples were analyzed:  5 small intestine biopsies, 7 paired biopsy samples of normal esophagus and Barrett's esophagus without dysplasia

first: Douglas

last: Stairs

first: Debra

last: Silberg

middle: W

last: Tobias


title: Transcription profiling of Arabidopsis dor mutant and wild-type plants in response to drought stress.

status: Public on Sep 25 2008

city: Beijing

first: Wenying

last: Xu

address: Datun Road, Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences

summary:
ATH1 GeneChip was used for gene expression analysis of wild-type plants and dor mutant under drought treatment (both the wild-type and dor plants were grown under normal watering conditions for 24 days and then stressed by completely depriving of irrigation for 10 days). Two biological repeat experiments were conducted and the raw data was analyzed applying Affymetrix GCOS software.
Keywords: both the wild-type and dor plants were grown under normal watering conditions for 24 days and then stressed  for 10 days

first: Y

first: Zhonghui

last: Li

first: Xing

last: Deng

first: Weihua

last: Wu

first: Yongbiao

last: Xue


title: Expression Analysis of Juvenile Pilocytic Astrocytomas by Oligonucleotide Microarray Reveals Two Potential Subgroups

city: Houston

first: Kwong-Kwok

last: Wong

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

summary: Juvenile pilocytic astrocytoma (JPA) is one of the most common brain tumors in children. The expression profiles of 21 JPAs, determined using Affymetrix GeneChip U133A, were compared with subjects with normal cerebella. The genes involved in neurogenesis, cell adhesion, synaptic transmission, central nervous system development, potassium ion transport, protein dephosphorylation, and cell differentiation were found to be significantly deregulated in JPA. These 21 JPAs were further clustered into two major groups by unsupervised hierarchical clustering using a set of 848 genes with high covariance (0.5-10). Supervised analysis with Significance Analysis of Microarrays software between these two potential subgroups identified a list of significant differentially expressed genes involved in cell adhesion, regulation of cell growth, cell motility, nerve ensheathment, and angiogenesis. Immunostaining of myelin basic protein on paraffin sections derived from 18 incompletely resected JPAs suggests that JPA without myelin basic protein–positively stained tumor cells may have a higher tendency to progress.

overall_design: Under an Institutional Review Board–approved protocol, brain tumor tissues were obtained, after informed consent, from patients undergoing tumor resection or other tumor-related neurosurgical procedures at the Texas Children's Hospital, Baylor College of Medicine. Samples of normal cerebellar tissue (n = 2) were isolated from surgically removed tissue adjacent to resected tumor tissue. Portions of the tumors were fixed in 10% formaldehyde and embedded in paraffin for sectioning and pathologic reviews, and the residual tissue samples were snap-frozen in liquid nitrogen and stored at –80°C for RNA extraction. All samples were obtained at initial diagnosis with no prior exposure to chemotherapy or radiation therapy. Normal fetal brain RNA was obtained from Stratagene (La Jolla, CA) and a normal cerebellum RNA was from Ambion, Inc. (Austin, TX). Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) followed by DNase I treatment and clean-up on aRNeasy spin column (Qiagen, Valencia, CA). RNA quality and purity were assessed by agarose gel electrophoresis and absorbance measurement at A260/A280.

first: Yi-Mieng

last: Chang

first: Yvonne

last: Tsang

first: Laszlo

last: Perlaky

first: Adkunle

last: Adesina

first: Dawna

last: Armstrong

first: Meenakshi

last: Bhattacharjee

first: Robert

last: Dauser

first: Susan

last: Blaney

first: Murali

last: Chintagumpala

first: Ching

middle: C

last: Lau


title: C. fulvum Avr2

status: Public on Oct 02 2008

city: Wageningen

first: Bart

last: Thomma

state: Gelderland

address: Binnenhaven 5

department: Plant Sciences

institute: Wageningen University

summary:
Heterologous expression of the fungal pathogen Cladosporium fulvum Avr2 in Arabidopsis plants.
Keywords: plant disease

overall_design: Samples used for microarray analyses were replicated three times in independent experiments and each replication consisted of 10 Avr2-expressing Arabidopsis plants and 10 Col-0 plants grown for four weeks under standard greenhouse conditions

first: Peter

last: van Esse

last: van Baarlen


title: Differential response of gun mutants to norflurazon

status: Public on Sep 23 2008

city: La Jolla

first: Joanne

last: Chory

address: 10010 N. Torrey Pines Road.

department: Plant Biology Laboratory

institute: The Salk Institute for Biological Studies

summary:
Analysis of the genome wide response of wild type and two mutant arabidopsis thaliana seedlings to norflurazon

Keywords: Genome wide response to inhibition of chloroplast development

overall_design: 5 day old seedlings of wild type (Col-0) and two mutants (gun1-9 and gun5). Three biological replicates for untreated or treated seedlings.

first: Ajit

last: Nott

first: Shai

last: Koussevitzky

first: Todd

last: Mockler

first: Fangxin

last: Hong


title: EZH2 is a mediator of EWS-FLI1 driven tumor growth blocking endothelial and neuro-ectodermal differentiation

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charité - Universitätsmedizin Berlin

summary: Ewing Tumors (ET) are highly malignant tumors, localized in bone or soft tissue and are molecularly defined by ews/ets translocations. We identified histone methyl-transferase Enhancer of Zeste, Drosophila, Homolog 2 (EZH2) to be increased in ET. EZH2’s suppressive activity maintains stemness in normal and malignant cells. Here we found EZH2 to be upregulated by the pathognomonic fusion oncogene EWS-FLI1 in ET and mesenchymal stem cells. Downregulation of EZH2 by RNA interference in ET suppressed oncogenic transformation by inhibiting clonogenicity in vitro. Similarly, tumor development and metastasis in immunodeficient Rag2-/-γC-/- mice was suppressed. EZH2-mediated gene silencing was shown to be dependent on histone deacetylase (HDAC) activity. Subsequent microarray analysis of EZH2 knock down, HDAC-inhibitor treatment and confirmation in independent assays revealed an undifferentiated phenotype maintained by EZH2 in ET. Downregulation of EZH2 decreased histone H3 lysine 27 trimethylation (H3K27me3) at target loci. EZH2 regulated stemness genes such as nerve growth factor receptor (NGFR) as well as genes involved in neuroectodermal differentiation (EMP1, EPHB2, GFAP, GAP43). These data suggest that EZH2 might play a central role in Ewing Tumor pathology shaping the oncogenicity and stem cell phenotype of this tumor presumably by epigenetic regulation.

overall_design: A673 cells were treated for 24 hours either with 100 nM Trichostatin A (TSA) or 0.01% DMSO. In siRNA experiments with ezh2 specific siRNA A673 cells were resuspended in medium containing 5 nM siRNA and transfection reagent and incubated for 48 hours. RNA from cells under such treatment was isolated with Trizol and subjected to microarray analysis onto human U133A microarray following the Affymetrix protocol.

middle: H

first: Sabine

last: Roessler

first: Martin

middle: S

last: Staege

first: Stefan

last: Burdach


title: Organ regeneration in plants is independent of stem cell niche activity

status: Public on Oct 30 2008

city: New York

first: Kenneth

middle: David

last: Birnbaum

address: 12 Waverly Place

department: Biology

institute: New York University

summary:
A critical step in regeneration is recreating the cellular identities and patterns of lost organs long after embryogenesis is complete. In plants, perpetual (indeterminate) organ growth occurs in apical stem cell niches, which have been shown to re-establish quickly when damaged or removed (1,2). Here we ask whether the machinery of perpetual organ growth, stem cell activity, is needed for the phase of regeneration that leads to replenishing lost cell identities and patterning, or, whether organ re-establishment enlists a wider group of pluripotent cells. We adapt a root tip regeneration system to Arabidopsis that permits us to assess the molecular and functional recovery of specific cell fates during organ regeneration. These results suggest a rapid restoration of missing cell fate and function in advance of the recovery of stem cell activity. Surprisingly, plants with mutations that fail to maintain stem cell activity were able to re-pattern their distal tip and re-specify lost cell fates. Thus, although stem cell activity is required to resume indeterminate growth (3), our results show it is not necessary for cell re-specification and patterning steps. This implies a regeneration mechanism that coordinates patterning of the whole organ, as in embryogenesis, but is initiated from different starting morphologies.  1. Feldman, L. J. Denovo Origin of Quiescent Center Regenerating Root Apices of Zea-Mays. Planta 128, 207-212 (1976).  2. Xu, J. et al. A molecular framework for plant regeneration. Science 311, 385-8 (2006).  3. Gordon, S. P. et al. Pattern formation during de novo assembly of the Arabidopsis shoot meristem. Development 134, 3539-48 (2007).
We adapted root tip excision techniques to Arabidopsis, enabling us to perform microarray profiling of regenerating root tissue. Excisions were performed at 4 days post-germination (dpg) at a distance of 130 um from the root tip, resulting in the complete excision of QC, all surrounding stem cells along with several tiers of daughter cells, and the root cap, including all of the columella and most of the lateral root cap. The tip section and then approximately 70 um of regenerating tissue was recut at different time points post cutting. We sampled regenerating stumps at 0hrs, 5 hrs, 13 hrs, 22 hrs, and 7 days after the excision for microarray analysis (Methods). We also sampled root sections immediately above the zone competent to regenerate at 270 um to approximately 340 um.
Keywords: time course, development, root regeneration

overall_design: 30 samples with 4 or 3 replicates for each condition representing a time course of regenerating root stumps and including controls for root tips (regeneration endpoint) at 4 dpg and 8 dpg and a wounded set of samples representing root tissue at 270-340 mm from the root tip for non-regeneration control

first: Giovanni

last: Sena

first: Xiaoning

last: Wang

first: Hsiao-Yun

last: Liu


title: Knockdown and overexpression of CIN-TCP genes

status: Public on Sep 17 2008

city: Rehovot

first: Idan

middle: D.

last: Efroni

address: Weizmann

institute: Weizmann Institute

summary: Leaf development has been monitored chiefly by following anatomical markers. Analysis of transcriptome dynamics during leaf maturation revealed multiple expression patterns that rise or fall with age or that display age specific peaks. These were used to formulate a digital differentiation index (DDI), based on a set of selected markers with informative expression during leaf ontogeny. The leaf-based DDI reliably predicted the developmental state of leaf samples from diverse sources and was independent of mitotic cell division transcripts or propensity of the specific cell type. When calibrated by informative root markers, the same algorithm accurately diagnosed dissected root samples. We used the DDI to characterize plants with reduced activities of multiple CINCINNATA (CIN)-TCP growth regulators. These plants had giant curled leaves made up of small cells with abnormal shape, low DDI scores and low expression of mitosis markers, depicting the primary role of CIN-TCPs as promoters of differentiation. Delayed activity of several CIN-TCPs resulted in abnormally large but flat leaves with regular cells. The application of DDI has therefore portrayed the CIN-TCPs as heterochronic regulators that permit the development of a flexible and robust leaf form through an ordered and protracted maturation schedule.

overall_design:
Vegetative apices of arabidopsis plants from modified CIN-TCP activity were collected.
1. Overexpression of an artificial microRNA targeting TCP5, TCP13 and TCP17
2. Overexpression of the endogenous microRNA 319b targeting TCP2, TCP3, TCP4, TCP10 and TCP24
3. the combination of the two microRNA, knocking down the eight CIN-TCP
4. Overexpression of TCP4 under the leaf specific BLS promoter

first: Yuval

last: Eshed

first: Eyal

last: Blum


title: Penetration resistance: Wildtype and ataf1-1 mutant response to Bgh 12 h after inoculation, 2*2 factorial design

status: Public on Sep 20 2008

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: Arabidopsis is a non-host to the biotrophic fungus Blumeria graminis f.sp. hordei (Bgh), effectively hindering Bgh ingress to the epidermal cells by deposition of callosic papillae formations, i.e. penetration resistance. To better understand the transcriptional changes in Arabidopsis towards Bgh, we compared un-inoculated and inoculated wild-type Arabidopsis samples, with those an ATAF1 mutant allele, compromised in penetration resistance. The experiment included sampling of 8 rosettes for each replicate sample from 6-weeks old plants, 12 hrs after inoculation. A total of 12 biolocigal replicates were sampled with three replicates from each of the four blocks (Wild-type, ataf1-1, Bgh, control).   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Michael Krogh Jensen.  The equivalent experiment is AT31 at PLEXdb.]

overall_design: genotype: Wild-type Arabidopsis, ecotype Col-0 - treated or untreated: Un-inoculated(3-replications);  genotype: Wild-type Arabidopsis, ecotype Col-0 - treated or untreated: Bgh inoculated(3-replications);  genotype: ataf1-1 mutant, ecotype Col-0 - treated or untreated: Un-inoculated(3-replications);  genotype: ataf1-1 mutant, ecotype Col-0 - treated or untreated: Bgh inoculated(3-replications)

first: Michael

last: Jensen


title: FNR1 mutation against ecotype variation

status: Public on Oct 11 2008

city: suita

first: Guy

middle: Thomas

last: Hanke

state: Osaka

address: 3-2 Yamadaoka

department: Institute for Protein Research

country: Japan

institute: Osaka University

summary:
The mechanism by which plants regulate channeling of photosynthetically derived electrons into different areas of chloroplast metabolism remains obscure. In higher plants, these electrons are made accessible to stromal enzymes, or cyclic electron flow, as reduced ferredoxin (Fd), or NADPH. We investigated how the specific loss of an Arabidopsis (Arabidopsis thaliana) ferredoxin:NADPH reductase (FNR) isoprotein affected channeling of photosynthetic electrons into NADPH and Fd dependent metabolism.
Affymetrix gene chip comparison of transcript changes in these mutants against two different ecotype backgrounds indicates that stress signaling is perturbed, and experiments revealed that the mutants are more susceptible to oxidative stress.
Keywords: mutant wild type transcript profile comparison

overall_design: We isolated arabidopsis mutants of the FNR1 gene in different ecotypes, extracted RNA from these and respective wild type plants and hybridised it to Affymetrix microarrays

middle: T

first: Toshiharu

last: Hase


title: Comparison of stimulatory and inhibitory dendritic cell subsets reveals new role of DC in granulomatous infection

status: Public on Oct 21 2008

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary:
Myeloid dendritic cells (DC) and macrophages play an important role in pathogen sensing and antimicrobial defense. Recently we demonstrated that infection of human DC with intracellular bacterium Listeria monocytogenes (L.monocytogenes) leads to the induction of the immunoinhibitory enzyme indoleamine 2,3-dioxygenase (Popov et al., J Clin Invest, 2006), while in the previous studies L.monocytogenes infection was associated with a rather stimulatory DC phenotype. To clarify this discrepancy we performed comparative microarray analysis of immature mo-DC (immDC), mature stimulatory mo-DC (matDC) and mature inhibitory DC either stimulated with prostaglandin E2 (PGE2-DC) or infected with L.monocytogenes (infDC). Studying infection of human myeloid DC with Listeria monocytogenes, we found out, that infected DC are modified by the pathogen to express multiple inhibitory molecules, including indoleamine 2,3-dioxygenase (IDO), cyclooxygenase-2, interleukin 10 and CD25, which acts on DC as IL-2 scavenger. All these inhibitory molecules, expressed on regulatory DC (DCreg), are strictly TNF-dependent and are in concert suppressing T-cell responses. Moreover, only DCreg can efficiently control the number of intracellular listeria, mostly by IDO-mediated mechanisms and by other factors, remaining to be identified. Analyzing publicly acessible data of transcriptional changes in DC and macrophages, infected by various pathogens and parasites (GEO, GSE360), we noticed that infection of these cells with Mycobacterium tuberculosis causes transcriptional response, comparable with the one caused by listeria in human DC. In fact, granuloma in tuberculosis and listeriosis in vivo are enriched for myeloid DC and macrophages characterized by regulatory phenotype.
In summary, regulatory myeloid DC and macrophages may play a dual role during life-threatening granulomatous infections, such as tuberculosis: on one hand, regulatory myeloid cells promote pathogen containment by efficiently killing intracellular bacteria, on the other hand these cells inhibit granuloma-associated T cells and thereby might be involved in the retention of TNF-controlled granuloma integrity protecting the host from granuloma break-down and pathogen dissemination.
Keywords: Cell type comparison, response to infection

overall_design: Transcriptional profiles of immature mo-DC (immDC, n=3), mature stimulatory mo-DC (matDC, n=3) and mature inhibitory mo-DC either stimulated with prostaglandin E2 (PGE2-DC, n=3) or infected with L.monocytogenes (infDC, n=3) were compared on Affymetrix HG-U133A platform. All samples represent biological replicates and were processed separately throughout the experiment.

first: Alexey

last: Popov

middle: L


title: SOX4 effect on LNCaP prostate cancer cells

status: Public on Nov 10 2008

city: Atlanta

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression changes in passage 1 mesenchymal stem cells from bone marrow stroma during 15 day culturing

status: Public on Sep 19 2008

city: Temple

first: Joni

last: Ylostalo

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

summary: To study the gene expression changes in mesenchymal stem cells from bone marrow stroma (MSCs) during in vitro expansion (from low density), passage 1 MSC were grown in culture for 15 days with medium change every 2-3 days. Samples for microarrays were taken at day 5 (early log-phase), 10 (late log-phase) and 15 (stationary phase). The data was queried for expression changes in Wnt signaling molecules and cell surface markers. Several components of the canonical Wnt signaling pathway were expressed, including Dkk-1; Wnt-5a; alpha-catenin; beta-catenin; frizzled 1, 4, 6, and 7; disheveled; glycogen synthetase kinase 3 beta; and glycogen synthetase kinase 3 alpha. In addition, the expression of over 10 cell surface transcripts decreased and an almost equal number increased during expansion.  The two of the transcripts with the largest decreases coded for proteins previously shown to be linked to cell motility and tumor progression: PODXL, and alpha6-integrin (CD49f). As the cultures expanded, the largest increase was for mRNA for the cell adhesion protein VCAM-1. To study the gene expression changes in more detail, real-time RT-PCR, RT-PCR, ELISAs, FACS, and western blotting were performed for additional MSC donors. The results demonstrated dramatic changes in the transcriptome of MSCs during in vitro expansion.

overall_design: Cells from one MSC donor were used for expansion in vitro and samples were taken at day 5, 10, and 15. Total of 3 samples were run on microarrays (day 5, 10 and 15).

first: Carl

middle: A

last: Gregory


title: Human dendritic cells treated with Echinacea purpurea phytocompounds

status: Public on Sep 10 2008

first: Ning-Sun

last: Yang

state: Taiwan

address: No.128 Sec.2, Academia Rd.

department: Agricultural Biotechnology Research Center

institute: Academia Sinica

summary: This study investigated the specific and differential gene expression in human immature DCs (iDCs) in response to treatment with a butanol fraction containing defined bioactive phytocompounds extracted from stems and leaves of Echinacea purpurea

overall_design: Human immature DCs (iDCs) differentiated from primary monocytes in vitro were incubated with [BF/S+L/Ep] or cichoric acid for 4 or 24 h to characterize early- or late-responsive genes. A total of nine Affymetrix HU-133A chips were hybridized to determine the transcriptome profiles in human iDCs.

first: Chien-Yu


title: Renal Proximal Tube Epithelial Cells at 24h and 1% oxygen

city: Copenhagen

first: Peter

last: Staller

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: Aim of the study was to characterize the transcriptional response of human primary renal proximal tubule epithelial cells (RPTEC) to low oxygen stress.

overall_design: Passage 4 renal proximal tubule epithelial cells were exposed to a humidified atmosphere consisting of either 5% CO2 and 95% air (20% O2, normoxia) or 5% CO2, 1% oxygen and 95% nitrogen (hypoxia) for 24 hours. Total RNA was extracted immediately after exposure. Three independent biological replicates were performed, resulting in 6 samples (3 control and 3 low oxygen).

first: Sophie

last: Beyer

first: Jens

middle: V

last: Johansen

first: Wilhelm

last: Krek

first: Edward

middle: J

last: Oakeley


title: Expression data from CD34+CD38- stem cells and more differentiated CD34+CD38+ progenitor cellsmbryo

city: Leiden

first: Arnolda

last: de Nooij-van Dalen

address: Albinusdreef 2

department: Hematology

institute: LUMC

summary:
Gene expression profiles of CD34+CD38- stem cells and more differentiated CD34+CD38+ progenitor cells were compared. Comparison of expression profiles of hematopoietic stem cells from fetal liver, umbilical cord blood, bone marrow and mobilized pheripheral blood allowed us to identify a unique set of genes with conserved expression during ontogeny.
Keywords: Cell type comparison

overall_design: CD34+CD38- en CD34+CD38+ cell populations were isolated by cell sorting from human Bone Marrow, mobilized peripheral blood, umbilical cord blood and fetal liver. Total RNA was isolated from each cell population followed by the synthesis of biotinylated cRNA. After fragmentation the biotinylated cRNA was hybridized to affymetrix U133A chips.

first: Willem

last: Fibbe

first: Sicco

last: Scherjon

first: Roel

last: Willemze

first: R

last: Barge


title: ISWI RNAi in Drosophila SL2 cells

status: Public on Sep 05 2008

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary:
Profiling of changes in steady state RNA levels upon RNAi-mediated knockdown of the nucleosome remodeling ATPase ISWI in Drosophila SL2 cells.
Quantitation of the corresponding proteomes has been performed to describe transcriptome-proteome relations. The analysis indicates a limited correlation of the two expression steps.
Keywords: RNAi-mediated knockdown

overall_design: Drosophila SL2 cells were incubated 7 days after treatment with 10 µg of dsRNA directed against GST or ISWI, respectively. 3 biological replicates per experimental conditions have been collected.

first: Tiziana

last: Bonaldi

first: Chanchal

last: Kumar

first: Juergen

last: Cox

middle: B

last: Becker

first: Matthias

last: Mann


title: Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis

status: Public on Sep 08 2008

first: Wei-Hua

last: Wu

state: Beijing

address: No.2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

summary: Pollen germination, along with pollen tube growth, is an essential process for the reproduction of flowering plants.  The germinating pollen with tip-growth characteristics provides an ideal model system for the study of cell growth and morphogenesis.  As an essential step towards a detailed understanding of this important process, the objective of this study was to comprehensively analyze the transcriptome changes during pollen germination and pollen tube growth.  Using Affymetrix Arabidopsis ATH1 Genome Arrays, this study is the first to show the changes in the transcriptome from desiccated mature pollen grains to hydrated pollen grains and then to pollen tubes of Arabidopsis thaliana.  The number of expressed genes, either for total expressed genes or for specifically expressed genes, increased significantly from desiccated mature pollen to hydrated pollen and again to growing pollen tubes, which is consistent with the finding that pollen germination and tube growth was significantly inhibited in vitro by a transcriptional inhibitor.  The results of GO analyses showed that expression of genes related to cell rescue, transcription, signal transduction and cellular transport were significantly changed, especially for up-regulation, during pollen germination and tube growth, respectively.  In particular, genes of the CaM/CML, CHX and Hsp families showed the most significant changes during pollen germination and tube growth.  These results demonstrate that the overall transcription of genes, both in the number of expressed genes and in the levels of transcription, was increased.  Furthermore, the appearance of many novel transcripts during pollen germination as well as tube growth indicates that these newly expressed genes may function in this complex process.

overall_design: Three samples are analyzed in this experiment.  They are desiccated mature pollen grains (MP), hydrated pollen grains (HP) and growing pollen tubes (PT) of Arabidopsis thaliana, respectively.  Each sample has two biological replicates, so that there are 6 data sets of ATH1 array in this experiment.

first: Yi

last: Wang

first: Wen-Zheng

last: Zhang

first: Lian-Fen

last: Song

first: Jun-Jie

last: Zou

first: Zhen

last: Su


title: Gene expression from human prefrontal cortex (BA46)

status: Public on Sep 03 2008

city: Wako

first: Kazuya

last: Iwamoto

address: 2-1 Hirosawa

department: Brain Science Institute

institute: RIKEN

summary:
Accumulating evidence suggests that mitochondrial dysfunction underlies the pathophysiology of bipolar disorder (BD) and schizophrenia (SZ). We performed large-scale DNA microarray analysis of postmortem brains of patients with BD or SZ, and examined expression patterns of mitochondria-related genes. We found a global down-regulation of mitochondrial genes, such as those encoding respiratory chain components, in BD and SZ samples, even after the effect of sample pH was controlled. However, this was likely due to the effects of medication. Medication-free patients with BD showed tendency of up-regulation of subset of mitochondrial genes. Our findings support the mitochondrial dysfunction hypothesis of BD and SZ pathologies. However, it may be the expression changes of a small fraction of mitochondrial genes rather than the global down-regulation of mitochondrial genes. Our findings warrant further study of the molecular mechanisms underlying mitochondrial dysfunction in BD and SZ.

Keywords: disease state analysis

overall_design: A total of 102 postmortem brains obtained from the Stanley Medical Research Institute were used for DNA microarray analysis. Fresh frozen samples were used for RNA extraction.

first: Miki

last: Bundo

first: Tadafumi

last: Kato


title: Global expression profiling of wild type and transgenic Arabidopsis plants in response to water stress

status: Public on Sep 01 2008

city: Raleigh

first: Imara

last: Perera

address: Campus Box 7612

department: Plant Biology

country: USA

institute: North Carolina State University

summary:
Transgenic Arabidopsis plants with constitutively low inositol (1,4,5) triphosphate exhibit an increased tolerance to water stress by an ABA-independent pathway
The phosphoinositide pathway and inositol (1,4,5) trisphopsphate (InsP3) are implicated in plant responses to stress. In order to manipulate the pathway and determine the downstream consequences of altered InsP3-mediated signaling, we generated transgenic Arabidopsis plants expressing the mammalian type I inositol polyphosphate 5-phosphatase, an enzyme that specifically hydrolyzes the soluble inositol phosphates and terminates the signal.  Transgenic plants have no morphological differences compared to wild type; however, rapid transient Ca2+ responses to a cold or salt stimulus are reduced by ~ 30%. To further understand the role of InsP3-mediated signaling in plant stress responses we focused on drought stress. Surprisingly, the InsP 5-ptase plants lose less water and exhibited an increased tolerance to drought. Stomatal bioassays showed that transgenic guard cells are less responsive to the inhibition of opening by ABA but show an increased sensitivity to ABA-induced closure. The onset of the drought stress is delayed in the transgenic plants and ABA levels did not increase as much as in the wild type. Transcript profiling has revealed that DREB2A and a subset of DREB2A regulated genes are basally up regulated in the InsP 5-ptase plants.  These results indicate that the drought tolerance of the InsP 5-ptase plants is mediated in part via an ABA-independent pathway. The constitutive dampening of the InsP3 signal in this system has uncovered novel regulation and cross talk between signaling pathways.
Keywords: drought stress, expression study

overall_design: In order to compare global expression profiles between wild type and transgenic plants in response to water stress we harvested leaves for transcript profiling at day 0 (well watered) and at day 7 when the transgenic plants were still at an RWC of >85%  and the wild type and vector control plants were at an RWC of ~ 50 -60% .  Leaves were harvested and pooled from ~ 10 plants of each line/time point and three independent biological replicates were carried out with wild type (WT) and 2 independent transgenic lines (T6 and T8).  The vector control line (C2) was used as an additional control.

middle: Y

first: Chiu-Yueh

last: Hung

first: Wendy

middle: F

last: Boss


title: Expression profiling of the overexpression of MILDEW-INDUCED LESIONS 4

city: Berkeley

first: Shauna

last: Somerville

address: 130 Calvin Hall, Mail Code 5230

department: Energy Biosciences Institute

institute: University of California at Berkeley

summary:
The 4 weeks old plant of genotype overexpression mil4 mutants were sprayed with BTH. The rosette tissue were collected for RNA expression profiling.
Keywords: defense response

overall_design: The rosettes were collected when the plants were 4 weeks old for RNA extraction and hybridization on Affymetrix microarrays.

first: Marc

last: Nishimura

first: Bi-Huei

last: Hou


title: Transcriptome analysis of the Arabidopsis phloem

city: Wuerzburg

first: Rosalia

last: Deeken

address: Julius-von-Sachs-Platz 2

department: Department of Molecular Plant Physiology and Biophysics

institute: University of Wuerzburg, Julius-von-Sachs-Institute

summary:
This sudy focuses on the identification of transcripts in the shoot phloem of the model plant Arabidopsis thaliana. Transcripts expressed in the phloem tissue (parenchyma cell, companion cell, sieve element) were excised by laser microdissection pressure catapulting (LMPC). These were compared with transcripts isolated from leaf phloem exudates by EDTA-chelation technique. Optimization of sample harvest resulted in RNA of high quality from both sources. Modifications of the RNA amplification procedure obtained RNA of sufficient yield and quality for microarray experiments. Microarrays (Affymetrix, ATH1) hybridized with RNA derived from phloem tissue by LMPC or phloem sap allowed us to differentiate between phloem located and mobile transcript species. The datasets provide a search criterion for phloem-based signals and will facilitate reverse genetic studies and forward genetic screens for phloem and long distance RNA signaling mutants.
Keywords: profiles of mobile and stationary Arabidopsis phloem transcripts

overall_design: Arabidopsis plants were cultivated under short day conditions (8 h light) until flowering. Phloem tissue was isolated by Lasermicrodissection and Pressure Catapulting (LMPC) and phloem exudate by EDTA-chelation technique. In both experiments poly-A-RNA was extracted and amplified before hybridization of microarrays (Affymetrix, ATH1). For both experiments three LMPC-derived phloem tissue (LMPC-derived phloem_1-3) and three phloem exudate samples (Phloem exudate_1-3) were analysed. Precise protocols of plant growth, sample harvest, RNA extraction and amplification are provided in Deeken et al., 2008.

first: Peter

last: Ache

first: Inga

last: Kajahn

first: Joern

last: Klinkenberg

first: Gerhard

last: Bringmann

first: Rainer

last: Hedrich


title: Identification of inter-individual and gene-specific variances in mRNA expression profiles in the RA SM

status: Public on Sep 02 2008

city: Hannover

first: René

last: Huber

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Institute for Clinical Chemistry

institute: Hannover Medical School

summary:
Background. Rheumatoid arthritis (RA) is a chronic inflammatory and destructive joint disease, characterized by overexpression of pro-inflammatory/-destructive genes and other activating genes (e.g., proto-oncogenes) in the synovial membrane (SM). The gene expression in disease is often characterized by significant inter-individual variances via specific synchronization/ desynchronization of gene expression. To elucidate the contribution of the variance to the pathogenesis of disease, expression variances were tested in SM samples of RA patients, osteoarthritis (OA) patients, and normal controls (NC).
Results. For the comparison between RA and NC, 568 genes with significantly different variances in the 2 groups (p < 0.05; Bonferroni/Holm corrected Brown-Forsythe version of the Levene-Test) were selected. For the comparison between RA and OA, 333 genes were selected. Using the Kyoto encyclopedia of genes and genomes (KEGG), 10 pathways/complexes significantly affected by higher gene expression variances were identified in RA compared to NC, including cytokine – cytokine receptor interactions, the TGF-pathway, and anti-apoptosis.
Compared to OA, 3 pathways with significantly higher variances were identified in RA (e.g., B cell receptor signaling, VEGF signaling). Functionally, the majority of the identified pathways is involved in the regulation of inflammation, proliferation, cell survival, and angiogenesis.
Conclusion. In RA, a number of disease-relevant or even disease-specific pathways/complexes are characterized by broad intra-group, inter-individual expression variances. This indicates that RA pathogenesis in different individuals may depend to a lesser extent on common alterations of the expression of specific key genes, but on individual-specific alterations of different genes resulting in common disturbances of key pathways.

overall_design: Expression variances were tested in synovial membrane samples of rheumatoid arthritis patients, osteoarthritis patients, and normal controls (see publication for further details).

first: Christian

last: Hummert

first: Ulrike

last: Gausmann

first: Dirk

last: Pohlers

last: Koczan

first: Reinhard

last: Guthke

first: Raimund

middle: W

last: Kinne