title: Expression data from Drosophila S2 cells depleted of exosome subunits

city: Cleveland

first: Daniel

middle: Louis

last: Kiss

state: OH

address: 2109 Adelbert Road

department: Molceular Biology and Microbiology

institute: Case Western Reserve University

summary:
The exosome complex and its' subunits are vital for proccessing and or degrading many cellular RNAs.
We used microarrays to detail the global changes in mRNA levels in response to exosome subunit depletion.

overall_design: RNA was extracted from dsRNA treated S2 cells and hybridized using Affymetrix microarrays. We aimed to obtain a master set of mRNAs surveyed by exosme subunits in vivo.

last: kiss

first: Erik

last: Andrulis


title: Expression Profiling of Cellular Genes Modulated by Kaposi’s Sarcoma Associated Herpesvirus (KSHV) RTA/ORF50 in HEK293 Cells

status: Public on May 26 2010

city: Miaoli Conunty

first: Su-Fang

last: Lin

address: No 35, Keyan Road, Zhunan Town

department: NICR

country: Taiwan

institute: National Health Research Institutes, Taiwan

summary:
KSHV RTA (K-RTA) is a transcriptional activator that functions to disrupt KSHV latency and activates specific sets of viral promoters in the lytic cycle. Structure-function studies indicate that K-RTA possesses a very potent transactivation domain locating at the C-terminus. To further characterize the biological functions of K-RTA, we have established three doxycycline-inducible K-RTA 293 cell lines using RevTRE/Tet-On system (Clontech). Comparing to two control lines in which K-RTA was replaced with luciferase reporter, a total of 88 host genes were identified to be modulated by 24 h doxycycline-induced K-RTA synthesized in 293 cells.
Designations for the three K-RTA inducible cell lines are KRta_92, KRta_116 and KRta_124; for the control line is RevTRE_Luc_1.

overall_design: All the four inducible cell lines were grown to log-phase before doxycycline induction. Same number of cells from the four cell lines were treated with doxycycline for 24 h . One duplicate of control RevTRE_Luc_1 was left untreated for inducer control. Total RNAs from the five samples were extracted and subjected to microarray analysis (Affymetrix HG-U133A, n=22,283). We sought to identify genes up- or down-regulated in the three doxycycline-treated K-RTA cells, but not in the treated or untreated RevTRE_Luc_1 cells.

first: Hsing-Jien

last: Kung


title: Human Nephrosclerosis Triggers a Hypoxia-Related Glomerulopathy

status: Public on Mar 30 2010

city: Ann Arbor

first: Preethi

last: Sankaranarayanan

state: MI

address: 1552 MSRB2,1150 W. Medical Center Drive

department: Department of Internal Medicine - Division of Nephrology

country: USA

institute: University of Michigan

summary: Expression data from microdissected glomeruli to examine the role of hypoxia in glomerulosclerosis of human Nephrosclerosis (NSC).

overall_design: Human Kidney biopsies of patients with NSC (n=14) and TN (n=4) were selected for RNA extraction and hybridization on Affymetrix microarrays. Gene expression data was then analysed using Genepattern and Genomatix software suites which revealed that CXCR4/CXCL12 plays a role in human NSC and therefore indicate that hypoxia contributes to glomerular damage in NSC.

first: Matthias

middle: A

last: Neusser

last: Kretzler


title: Gene expression variation in Y-substitution lines in different genetic backgrounds of Drosophila melanogaster

status: Public on May 08 2010

city: Cambridge

first: Pan-Pan

last: Jiang

state: MA

address: 16 Divinity Ave c/o Hartl Lab

department: Organismic and Evolutionary Biology

institute: Harvard University

summary: We studied Y chromosomes from two geographically diverse populations of Drosophila melanogaster, and show that these Y chromosomes differentially modify the expression of hundreds of autosomal and X-linked genes. Genes showing Y-linked regulatory variation also show an association with immune response and pheromone detection, as well as proximity to the X chromosome euchromatin-heterochromatin boundary.

overall_design: 4-6 dual channel arrays per background, with males carrying two Y geographically diverse chromosomes competitively hybridized to each array. Dye-swap design was used.

first: Bernardo

last: Lemos

middle: L

last: Hartl


title: Differentiation of Arabidopsis guard cells: analysis of the networks incorporating the basic helix-loop helix transcription factor, FAMA

status: Public on May 12 2010

city: Stanford

first: Dominique

last: Bergmann

state: CA

address: 371 Serra Mall

department: Biological Sciences

institute: Stanford University

summary: In plants, formation of functional stomatal guard cells is a highly regulated event so that this cell differentiation model constitutes an interesting genetic system to explore cell differentiation in response to cell cycle controllers or cell fate determinants such as transcription factors. The latest acting bHLH in the stomatal lineage circuit is FAMA that appears to be absolutely required to promote stomatal development by controlling the GMC to GC transition. In order for FAMA to trigger guard cell development, it probably initiates a gene activation cascade leading to cell differentiation and cessation of cell division. To identify and characterize FAMA inducible genes, transcriptome analysis using the Affymetrix ATH1 micro-array chip was carried out on inducible FAMA gain of function plants at 4hrs and 48 hrs post-induction.

overall_design: Transgenic plants with an estrogen-inducible FAMA expression cassette were used in a timecourse experiment to identify genes that were differentially regulated by FAMA. Two time points were analyzed, 4 hours and 48 hours post-induction. Seedlings were grown on vertically oriented plates in a 22 °C incubator under 24 hours light for 5 days. Plants were then transfered with forcepts to plates containing MS + Sucrose + 10 µM estrogen (or new MS + sucrose plates for controls). After 4h or 48h on new plates, samples were collected, frozen in liquid nitrogen and stored at –80 degree until enough material was obtained to do all RNA extractions in the same week. The Rneasy Plant Mini Kit (QIAGEN) for RNA isolation, and samples were labelled with standard kits, etc (get info) and hybridized to Affymetrix Ath1 array chips. 15 samples.

first: Kyoko

last: Ohashi-Ito

middle: C


title: Evaluation of the effects of 16p13.11 deletions on gene expression

status: Public on Mar 20 2010

city: New York

first: Erin

middle: L.

last: Heinzen

state: NY

department: Institute for Genomic Medicine

institute: Columbia University

summary: We analyzed seven epilepsy patients with a heterozygous chr16p13.11 deletion and eight controls with no deletion at this locus to evaluate the impact of the deletion on gene expression.

overall_design: Seven subjects with a 16p13.11 deletion compared to eight controls with no deletion at this locus, no replicates were performed.

first: David

middle: B

last: Goldstein


title: Biomarkers of human gastro-intestinal tract regions

city: Lausanne

first: James

last: Holzwarth

state: Vaud

address: vers chez les blanc

department: Bioanalytical Sciences

country: Switzerland

institute: Nestle Research Center

summary:
Background and aims: Dysregulation of intestinal epithelial cells performance associates with an array of pathologies whose onset mechanisms are incompletely understood. The aim of the present study was to provide a map of gene expresssion patterns along the human healthy adult gastro-intestinal tract and to implement a new procedure for microarray data noise filtering that would allow their use as a reference when screening for pathological deviations, such as inflammatory bowel disease (IBD).  Methods: Gene expression profiles in antrum, duodenum, jejunum, ileum and transverse colon biopsies were measured with the Affymetrix U133A array and principal component analysis was used to identify region-selective biomarkers. These data were intersected with highly variable genes from a public dataset of gene expression in the ileal and colonic healthy regions of UC and Crohn’s disease patients. Moreover, gene sets covering gut functions not entirely accounted for by the available public tools were constructed to monitor their expression along the GI tract.  Results: 166 genes were found to be responsible for distinguishing the five regions considered. Fourteen had never been described in the GI tract, including a semaphorin probably implicated in pathogen invasion, and six other novel genes. Similar analysis of the IBD datasets revealed that samples stratify based on disease rather than on the intestinal region. This withstanding, eleven genes were identified as possible early predictors of Crohn’s and/or UC in ileum and/or colon. These include CLCA4 and SLC26A2, both implicated in ion transport.   Conclusions: This novel approach, validated by retrieving known gene profiles, allowed the identification of promising new leads both in health and IBD state.
Keywords: gastro-intestinal tract comparison

overall_design: Biopsies were collected by endoscopy and colonoscopy from the antrum, duodenum, jejunum, ileum and transverse colon of two male and two female healthy human subjects, previous approval by the Ethical Committee of the Canton de Vaud, Lausanne, Switzerland. All surgical procedures were performed by a gastroenterologist at the University Hospital of the Canton de Vaud (CHUV), Lausanne, Switzerland. The individuals, informed about the scopes of the study, were aged 20-30 years, did not present any gastro-intestinal or cardio-vascular disorder, did not use any drug during 4 weeks before sampling and were Helicobacter pylori negative. The biopsies were snap-frozen and stored at –80 °C.

first: Elena

middle: M

last: Comelli

first: Sofiane

last: Lariani

first: Marie-Camille

last: Zwahlen

first: Grigorios

last: Fotopoulos

first: Robert

last: Mansourian

first: Christine

last: Cherbut

first: Gian

last: Dorta

first: Irène

last: Corthésy-Theulaz

first: Martin

last: Grigorov


title: Transcriptome Profiles of Early Organogenesis in Human Embryos and Integrative Mining for Underlying Molecular Network

status: Public on Mar 18 2010

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

country: United Kingdom

institute: University of Bristol

summary:
We here report transcriptome profiles of human embryos at six successive developmental stages (i.e., Carnegie Stages 9 to 14), representing the first comprehensive gene expression database of early human organogenesis.
         Through a series of data mining and comparisons with the transcriptome during mouse embryogenesis and the multi-layered genomic data in human embryonic stem cells, we revealed that development potential during early human organogenesis is orchestrated by two dominant categories of genes. Specifically, most gradually induced genes are largely differentiation-related and indicative of diverse organ formation, whereas those gradually repressed are involved in both stemness- and differentiation-relevant aspects of the developmental potential, which may be important for the initiation of organogenesis. Further through integrative mining we uncovered a molecular network (including a stemness-relevant module and a differentiation-relevant module) that may provide a framework for the regulation of early human organogenesis. Preliminary analysis of published data showed that the network could serve to evaluate various in vitro differentiation models.
        Our results make a significant step towards understanding of human embryogenesis at a molecular level and suggest that developmental potentials of early embryonic cells are under control of shared regulatory events.

overall_design:
With the consent of subjects and of the Ethical Review Board of the Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, we collected human post-implantation embryos at six successive time periods: Carnegie Stages 9 to 14 (E20 to E32), covering the first third of organogenesis.
       Using the Affymetrix HG-U133A Genechip microarrays, three replicates were independently profiled for each stage to minimize the influence of the embryo-to-embryo variation. Specifically, three biological replicates were conducted for embryos at S10 to S13; owing to practical limitations and material availability, embryos at S9 (S14) were pooled together, and their RNAs were extracted, split and then subjected to three technical replicate analyses. Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The resultant expression data were imported into Extraction of Differential Gene Expression (EDGE) software for the detection of probesets exhibiting the consistent changes within the triplicates and differential expression (denoted as hORG expression matrix). The hORG expression matrix was subjected to LIMMA bioconductor library for identification of stage-transitive transcriptome changes, and self-organizing map combined with singular value decomposition (SOM-SVD) as well as SOM-based two-phase gene clustering  for the topology-preserving extraction of temporal expression patterns (the software is available at http://www.cs.bris.ac.uk/~hfang/TPSC). Hypergeometric distribution-based enrichment analyses were performed to explore the underlying biological relevance of gene groups of interest using diverse external annotations (i.e., GOs, TFBSs, Mammalian Phenotypes, Diseasome). The Cytoscape plug-in jActiveModules was modified to identify expression-active connected subnetworks in the compiled human interaction/association network. See details in EXPERIMENTAL PROCEDURES and SUPPLEMENTAL INFORMATION.

first: Ying

last: Yang

first: Chunliang

last: Li

first: Shijun

last: Fu

first: Zhuqing

first: Gang

last: Jin

first: Kankan

last: Wang

first: Ji

last: Zhang


title: Identification of early flg22 responsive genes in Arabidopsis seedlings

city: Boston

first: Jen

last: Sheen

address: 185 Cambridge st. CPZN7620

department: Molecular Biology

institute: Massachusetts General Hospital

summary:
The goal of this experiment was to identify the early responsive genes activated by the 22 amino acid peptide of bacterial flagellin (flg22) in Arabidopsis seedlings that are involved in the initial responses important for plant innate immunity.
We used the microarrays to detail the global program of gene expression underlying intial cellular and molecular responses to microbial associated molecualr patterns (MAMPs).

overall_design: Arabidopsis seedlings were treated with 2 nM flg22 for 30 min and 60 min.  Transcript profiles were analyzed and compared between control and treated cells to identify early flg22 responsive genes.

first: Horim

last: Lee

first: Matthew

last: McCormack


title: Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Relatively little is understood about the dynamics of global host–pathogen transcriptome changes that occur during bacterial infection of mucosal surfaces. To test the hypothesis that group A Streptococcus (GAS) infection of the oropharynx provokes a host transcriptome response, we performed genome-wide transcriptome analysis using a nonhuman primate model of experimental pharyngitis. We also identified host and pathogen biological processes and individual host and pathogen gene pairs with correlated patterns of expression, suggesting interaction. For this study, 509 host genes and seven biological pathways were differentially expressed throughout the entire 32-day infection cycle. GAS infection produced an initial widespread significant decrease in expression of many host genes, including those involved in cytokine production, vesicle formation, metabolism, and signal transduction. This repression lasted until day 4, at which time a large increase in expression of host genes was observed, including those involved in protein translation, antigen presentation, and GTP-mediated signaling. The interactome analysis identified 73 host and pathogen gene pairs with correlated expression levels. We discovered significant correlations between transcripts of GAS genes involved in hyaluronic capsule production and host endocytic vesicle formation, GAS GTPases and host fibrinolytic genes, and GAS response to interaction with neutrophils. We also identified a strong signal, suggesting interaction between host γδ T cells and genes in the GAS mevalonic acid synthesis pathway responsible for production of isopentenyl-pyrophosphate, a short-chain phospholipid that stimulates these T cells. Taken together, our Q:2 results are unique in providing a comprehensive understanding of the host–pathogen interactome during mucosal infection by a bacterial pathogen.

overall_design:
Longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus

Briefly, animals were GAS-culture negative and had negligible antistreptolysin O titers, indicating no recent history of GAS exposure. Twenty animals were subjected to a mock-inoculation protocol (PBS only) for 5 weeks, rested for 4 weeks, and inoculated in the upper respiratory tract with 107 CFUsMGAS5005. Blood, saliva, and throat swabs were collected on days 0, 1, 2, 4, 7, 9, 16, 23, 32, 45, 58, 72, and 86. Only the first nine time-points were studied because specimens collected during days 0 to 32 had matching comparator specimens from the mock-infection protocol. Thirty-two clinical and laboratory parameters were measured by the same veterinarian during mock and infection periods.
Array data was only for the tonsil swabs, while blood and saliva used for other tests.

first: Patrick

middle: R

last: Shea

first: Kimmo

last: Virtaneva

first: John

middle: J

first: Stephen

middle: F

last: Porcella

first: William

middle: T

last: Barry

first: Fred

last: Wright

first: Scott

middle: D

last: Kobayashi

first: Aaron

last: Carmody

first: Robin

last: Ireland

first: Daniel

middle: E

first: Stacy

last: Ricklefs

first: Imran

last: Babar

first: Claire

last: Johnson

first: Morag

last: Graham

first: Donald

last: Gardner

last: Bailey

first: Michael

last: Parnell

first: Frank

last: DeLeo

first: James

last: Musser


title: A novel S-sulfocysteine synthase essential for chloroplast function in Arabidopsis thaliana

status: Public on Mar 31 2010

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

summary: In bacteria, the biosynthesis of cysteine is accomplished by two enzymes that are encoged by the cysK and cysM genes. CysM is also able to incorporate thiosulfate to produce S-sulfocysteine. In plant cells, the biosynthesis of cysteine occurs in the cytosol, mitochondria and chloroplasts. Chloroplasts contain two O-acetylserine(thiol)lyase homologs, which are encoded by the OAS-B and CS26 genes. An in vitro enzymatic analysis of the recombinant CS26 protein demonstrated that this isoform possesses S-sulfocysteine synthase activity and lacks O-acetylserine(thiol)lyase activity. In vivo functional analysis of this enzyme in knockout mutants demonstrated that mutation of cs26 suppressed the S-sulfocysteine synthase activity that was detected in wild type; furthermore, the mutants exhibited a growth phenotype, but penetrance depended on the light regime. The cs26 mutant plants also had reductions in chlorophyll content and photosynthetic activity (neither of which were observed in oas-b mutants), as well as elevated glutathione levels. However, cs26 leaves were not able to properly detoxify ROS, which accumulated to high levels under long-day growth conditions. The transcriptional profile of the cs26 mutant revealed that the mutation had a pleiotropic effect on many cellular and metabolic processes. Our finding reveals that S-sulfocysteine and the activity of S-sulfocysteine synthase play an important role in chloroplast function and are essential for light-dependent redox regulation within the chloroplast.

overall_design: Using the Affymetrix ATH1 GeneChips, we performed a comparative transcriptomic analysis on leaves of the cs26 and wild type plants under two different photoperiod conditions. Wild type and cs26 mutant plants were grown on soil under a long-day photoperiod (LD) or under a short-day photoperiod (SD). Total RNA was extracted from the leaves of 3-week-old plants grown under identical LD conditions, and from the leaves of 5-week-old plants grown under identical SD conditions. Three biological replicates were performed for each sample and hybridized to the chips. We made two different comparisons to classify the differently expressed genes in the mutant plant: cs26 leaves under LD versus wild-type leaves under LD and cs26 leaves under SD versus wild-type leaves under SD.

first: Maria

last: Bermúdez

first: Luis

last: Romero


title: Identification of CPK5ac and CPK11ac early target genes in Arabidopsis mesophyll cells

first: Jen

last: Sheen

summary:
The goal of this experiment was to identify the early target genes of constitutively activated CPK5ac and CPK11ac in Arabidopsis mesophyll cells that are involved in early flagellin responses important for plant innate immunity.
We used the microarrays to detail the global program of gene expression underlying initial calcium responses to microbial associated molecualr patterns (MAMPs).

overall_design: Arabidopsis mesophyll protoplasts were transfected with plasmid DNA to express constitutively active CPK5ac or CPK11ac for 6 hr.  Transcript profiles were analyzed and compared between cells transfected with control DNA and CPK5ac or CPK11ac DNA to identify early CPK5ac and CPK11ac target genes.

first: Matthew

last: Willmann

first: Marie

last: Boudsocq

first: Horim

last: Lee

last: McCormack


title: JAK2V617F mutation in CD34+ stem cells of essential thrombocythemia

status: Public on Apr 06 2010

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
The JAK2V617F mutation has been reported in about 40-60% of Essential Thrombocythemia (ET) patients. However, little is known about specific molecular abnormalities of the hematopoietic stem cell compartment of ET according to JAK2 mutation. Therefore, we compared the gene expression profiles of bone marrow (BM) CD34+ cells from 16 patients with and without the JAK2V617F mutation to identify differentially expressed genes.
Keywords: cell type comparison

overall_design:
Sample name and JAK2V617F mutation:
- BM CD34+ cells from healthy subject (CTR)
- ET JAK2V617F-positive: ET 1, ET 4, ET 6, ET 7, ET 8, ET 10, ET 12, ET 15
- ET JAK2V617F-negative: ET 2, ET 3, ET 5, ET 9, ET 11, ET 13, ET 14, ET 16

first: Lucia

last: Catani

first: Roberta

last: Zini

first: Sollazzo

last: Daria

first: Sergio

last: Ferrari

first: Roberto

last: Lemoli


title: Heterochromatin protein 1 (HP1) modulates replication timing of Drosophila heterochromatin

status: Public on Mar 16 2010

city: Vienna

first: Michaela

last: Schwaiger

address: Althanstr. 14

country: Austria

institute: University of Vienna

type: Genome binding/occupancy profiling by genome tiling array

summary:
The replication of a genomic region during S-phase can be highly dynamic between cell types that differ in transcriptome and epigenome. Replication timing has been positively correlated with several histone modifications that occur at active genes, while repressive histone modifications mark late replicating regions. This raises the question if chromatin modulates the initiating events of replication.  To gain insights into this question we have studied the function of heterochromatin protein 1 (HP1), a reader of to the repressive histone lysine 9 methylation of H3, in genome-wide organization of replication. Cells with reduced levels of HP1 show an advanced replication timing of centromeric repeats in agreement with the model that repressive chromatin mediates the very late replication of large clusters of constitutive heterochromatin. Surprisingly however regions with high levels of interspersed repeats on the chromosomal arms in particular on chromosome 4 and in pericentromeric regions of chromosome 2 behave differently. Here loss of HP1 results in delayed replication timing. The fact that these regions are bound by HP1 suggests a direct effect. Thus while HP1 mediates very late replication of centromeric DNA it is also required for early replication of autosomal regions with high levels of repeats.   This observation of opposing functions of HP1 suggests a model where repeat inactivation on autosomes is required for proper activation of origins of replication that fire early, while HP1 mediated repression at constitutive heterochromatin is required to ensure replication of centromeric repeats at the end of S phase.

Keywords: RNAi, chip-chip, replication timing

overall_design: RNA was isolated from Kc cells after knockdown of HP1 using RNAi (5 replicates) and hybridized to gene expression arrays. RNA was isolated from Kc cells after knockdown of HP1 using RNAi (2 replicates) and hybridised to tiling arrays. Early and late replicating DNA was isolated from Kc cells after knockdown of HP1 using RNAi  (2 replicates)  and hybridized to tiling arrays.  ChIP-chip was perfomred for H3K27me3 and H3K9me2 in Kc (2 replicates) cells.

first: Hubertus

last: Kohler

first: Edward

last: Oakeley

last: Stadler

first: Dirk

last: Schübeler


title: Subpopulations of CD163 positive macrophages are classically activated in psoriasis

status: Public on Mar 01 2010

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: To determine the transcriptional profile associated with macrophage polarization to M1 or M2, we cultured macrophages derived from monocytes for 7 days and treated them with IFNg, IL-4, TNF, LPS, and LPS+IFNg (n=7). Psoriasis lesional and non-lesional skin biopsies were included (n=5 pairs).

overall_design: Comparison of the transcriptome of psoriasis with cytokine-treated macrophages.

first: Judilyn

last: Fuentes-Duculan


title: Karrikin responses in Arabidopsis thaliana seed

city: Crawley

first: David

last: Nelson

state: WA

address: The University of Western Australia - M316

department: Plant Energy Biology

country: Australia

institute: University of Western Australia

summary: Karrikins promote seed germination in Arabidopsis thaliana. Completion of germination (protrusion of the radicle) is not observed until ~72 h in dormant wildtype seed under these conditions. We used microarrays to examine karrikin-induced transcriptional changes after 24 h of imbibition. Transcriptional changes may indicate events leading to karrikin-induced germination or karrikin-specific markers.

overall_design: Primary dormant seed of wildtype (which can germinate and is promoted by KAR1) and ga1-3 (which cannot germinate, and is not promoted by KAR1) were imbibed on water-agar or 1 uM KAR1 in the light at 20 C and assayed for gene expression after 24 h. Three or four biological replicates per genotype/treatment.

first: Steven

last: Smith


title: Transcriptional analysis of whole substantia nigra in Parkinson's disease

status: Public on Mar 12 2010

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: Post mortem tissue was dissected from two groups of age and gender matched groups of Parkinson and Control subjects

overall_design:
Published work contains more information on Parkinson and Control groups.

Samples GSM606624-GSM606626 are not included in the dataset described in PMID 15965975.

first: Michael

last: James

first: Yanli

last: Zhang

first: Richard

last: Davis


title: Transcriptional analysis of putamen in Parkinson's disease

overall_design:
Published work contains more information on Parkinson and Control groups.

Samples GSM606619-GSM606623 are not included in the dataset described in PMID 15965975.


title: Gene expression analysis of ovarian serous adenocarcinoma cell lines and tumors

status: Public on Feb 25 2010

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
A variety of human cancers demonstrate alterations in microRNA expression.  We hypothesized that regulatory defects in microRNAs play a central early role in organizing the molecular changes involved in ovarian cancer (OvCa).  Using both gene arrays and deep sequencing, we comprehensively profiled mRNA and microRNA expression, respectively, in human serous epithelial OvCa cell lines, serous tumors, and short-term primary cultures of normal ovarian surface epithelium (NOSE).  We expected that over-expression of a specific microRNA would lead to lower expression of its mRNA targets, and under-expression of a specific microRNA would lead to higher expression of its target genes.  Using our expression data in conjunction with established in silico algorithms, we found putative microRNA:mRNA functional pairs.

Keywords: two group comparison

overall_design: We generated gene expression profiles of a panel of seven OvCa serous cell lines, 17 serous tumors, and nine independent normal ovarian surface epithelium (NOSE) cultures.  We defined genes that were high or low in both cell lines and tumors relative to NOSE.

first: Marty

last: Matzuk

first: Preethi

last: Gunaratne

first: Matt

last: Anderson

first: Ankur

last: Nagaraja

last: Fountain


title: Ovarian serous cancer

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

overall_design: Refer to individual Series


title: The sexually antagonistic genes of Drosophila melanogaster

status: Public on Feb 10 2010

city: Uppsala

first: Paolo

last: Innocenti

address: Norbyvägen 18D

department: Dept. of Animal Ecology

country: Sweden

institute: Uppsala university

summary:
Differences in the selective pressures experienced by males and females are believed to be ubiquitous in dioecious organisms and are expected to result in the evolution of sexually antagonistic alleles, thereby driving the evolution of sexual dimorphism. Negative genetic correlation for fitness between the sexes has been documented, however, the identity, number and location of loci causing this relationship are unknown.
Here we show that a large proportion of Drosophila melanogaster transcripts are associated with the interaction between genomic haplotype and gender and that at least 8% of loci in the fly genome are currently evolving under sexually antagonistic selection.

overall_design:
We measured gene expression of adult males and females of Drosophila melanogaster from 15 hemiclone lines, showing either high-male/low-female fitness, high-female/lowmale fitness or average fitness in both sexes.

Data from four replicates for each sex/line are presented, giving a total of 120 arrays.

middle: H

last: Morrow


title: A MicroRNA Expression Signature For Cervical Cancer Prognosis

status: Public on Feb 15 2010

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

summary: In this study, we have identified a microRNA-based signature for the prediction of cervical cancer survival. MicroRNAs (miRNAs) are a newly identified family of small non-coding RNAs that are extensively involved in human cancers. Using our recently established PCR-based miRNA assays, we have analyzed 102 cervical cancers and identified two miRNAs (miR-200a and miR-9) that are likely to predict patient survival. A logistic regression model was developed based on these two miRNAs and the prognostic value of the model was subsequently validated with 42 independent cervical cancers. Furthermore, functional studies were performed to characterize the effect of miRNAs in cervical cancer cells. Our results suggest that both miR-200a and miR-9 could play important regulatory roles in cervical cancer control. In particular, miR-200a is likely to affect the metastatic potential of cervical cancer cells by simultaneously suppressing the expression of multiple genes that are important to cell motility.

overall_design: There are five arrays included in this experiment, including one negative control, one mock control, and three arrays to profile for the effects of miRNA overexpression in HeLa cells. Two miRNAs, miR-200a and miR-9 were analyzed.


title: Identification of transcripts harboring premature termination codons by NMD inhibition in a  panel of CCRCC cell lines

city: Groningen

first: Gerben

last: Duns

address: Oostersingel, ingang 47, 2nd floor, room E2.036

country: Netherlands

institute: Genetics Department, Groningen University

summary:
Identification of transcripts harbouring premature termination codons by NMD inhibition (GINI method) in a  panel of clear cell renal cell carcinoma cell lines.

Sporadic clear cell renal cell carcinoma (cRCC) is genetically characterized by the recurrent loss of chromosome 3p, with a hotspot for copy number loss in the 3p21 region. In this study, we applied a method called Gene Identification by Nonsense Mediated mRNA decay Inhibition (GINI) on a panel of 10 cRCC cell lines with 3p21 copy number loss to identify biallelic inactivated genes located at 3p21. This analysis revealed inactivation of the histone methyltransferase gene SETD2, located on 3p21.31, as a common event in cRCC cells. SETD2 is nonredundantly responsible for trimethylation of the histone mark H3K36. Consistent with this function, we observed loss or decrease of H3K36me3 in 7 out of 10 cRCC cell lines. Identification of missense mutations in 2 of 10 primary cRCC tumor samples further supported the involvement of loss of SETD2 function in the development of cRCC tumors.

overall_design: GINI (Gene identification by Nonsense mediated mRNA decay Inhibition) was applied to a panel of 10 clear cell renal cell carcinoma cell lines. Cells were treated with emetine, caffeine or were not treated. Experiments were performed in duplo (biological replicates). Gene expression was measured in two proximal tubular epithelial cell lines (in duplo, biological replicates) to assess expression in the  normal situation. Two different matrixes are shown: one that contains the data from the GINI experiment, the other contains the transcript levels in untreated cRCC and PTEC cells.

first: Inge

last: Van Duivenbode

first: Klaas

last: Kok


title: Cadherin-11 depletion in aggressive MDA-MB-231 breast cancer cells.

status: Public on Feb 22 2010

city: Washington

first: Jaime

last: Guidry Auvil

state: DC

address: 3970 Reservoir Road, NW

department: Lombardi Comprehensive Cancer Center

institute: Georgetown University Medical Center

summary: Cadherin-11 expression is associated with tumor progression and metastasis in various cancers, including basal-like breast carcinoma and advanced prostate cancer, and invasive cell lines, yet is absent in normal epithelium.  We now show cadherin-11 attenuation in aggressive breast and prostate cancer cells results in marked decreases in proliferation, migration, and invasion.  Cadherin-11 depletion in MDA-231 cells prevents tumor growth in mice and alters gene expression associated with poor prognosis malignancies.  Additionally, a novel small molecule inhibitor targeting its unique adhesive interface significantly inhibits the growth and migration of cadherin-11 positive cells.  Cadherin-11 is essential for malignant progression of MDA-231 basal-type cells, and may serve as both an aggressive tumor marker and viable therapeutic target for poor prognosis carcinomas expressing it.

overall_design: Seven microarray samples (3 empty vector controls--RNAi 1B, 4 siRNA treated targeting cadherin-11 wt isoform--RNAi 4A and 6A) were tested in pooled stable siRNA-expressing MDA-MB-231 breast cancer cells to potentially identify significant factors affected when cadherin-11 is depleted in aggressive breast cancer cells.  Cadherin-11 appears to play a role in certain poor prognosis, basal-like cancers, however little is known about its regulation.  This portion of our study was used to determine what genes may be regulated by cadherin-11 in breast cancer cells, as well as possible insights into mechanisms involved.

first: Stephen

middle: W

last: Byers

first: Constanze

last: Hampl

first: Siva

last: Dakshanamurthy

first: Milton

last: Brown

first: Habtom

last: Ressom

first: James

last: Li


first: Frank

last: Middleton

summary:
Transcriptional analysis of multiple brain regions in Parkinson's disease supports the involvement of specific protein processing, energy metabolism, and signaling pathways, and suggests novel disease mechanisms.

This SuperSeries is composed of the SubSeries listed below.


title: Gene expression analyses of mir-182 knockdown in ovarian clear cell cancer cell line

status: Public on Jan 28 2010

first: Chad

last: Creighton

summary:
A variety of human cancers demonstrate alterations in microRNA expression.  We hypothesized that regulatory defects in microRNAs play a central early role in organizing the molecular changes involved in ovarian cancer (OvCa).  Using both gene arrays and deep sequencing, we comprehensively profiled mRNA and microRNA expression, respectively, in human clear cell epithelial OvCa cell lines and short-term primary cultures of normal ovarian surface epithelium.  We expected that over-expression of a specific microRNA would lead to lower expression of its mRNA targets, and under-expression of a specific microRNA would lead to higher expression of its target genes.  Using our expression data in conjunction with established in silico algorithms, we found putative microRNA:mRNA functional pairs.  Furthermore, gene expression profiles were taken of clear cell cultures having functional knockdown or over-expression of specific microRNAs of interest.  Knockdown of mir-182 (found over-expressed in clear cell OvCa) resulted in up-regulation in vitro of a significant number of the in silico predicted mir-182 target genes that were normally under-expressed in OvCa.

Keywords: two group comparison; gene expression profiling

overall_design: We used miRNA mimics to knockdown expression of mir-182, which was over-expressed (fold>8) in OvCa clear cell cultures versus NOSE, using the clear cell line ES2.  After 48 hours of mimic treatment, we profiled for gene expression both cells with mir-182 knockdown and cells with mimic control (having minimal sequence identity with all human miRNAs).

first: Marty

last: Matzuk

last: Gunaratne

last: Anderson


title: Transcriptional analysis of prefrontal area 9 in Parkinson's disease

status: Public on Feb 04 2010

overall_design: Published work contains more information on Parkinson and Control groups

first: Michael

last: James

first: Yanli

last: Zhang

first: Richard

last: Davis


title: Gene expression analyses of mir-31 overexpression in ovarian serous cancer cell line

summary:
A variety of human cancers demonstrate alterations in microRNA expression.  We hypothesized that regulatory defects in microRNAs play a central early role in organizing the molecular changes involved in ovarian cancer (OvCa).  Using both gene arrays and deep sequencing, we comprehensively profiled mRNA and microRNA expression, respectively, in human serous epithelial OvCa cell lines, serous tumors, and short-term primary cultures of normal ovarian surface epithelium (NOSE).  We expected that over-expression of a specific microRNA would lead to lower expression of its mRNA targets, and under-expression of a specific microRNA would lead to higher expression of its target genes.  Using our expression data in conjunction with established in silico algorithms, we found putative microRNA:mRNA functional pairs.  Furthermore, gene expression profiles were taken of serous cultures having functional knockdown or over-expression of specific microRNAs of interest.  Over-expression of mir-31 (found under-expressed in serous OvCa) resulted in down-regulation in vitro of a significant number of the in silico predicted mir-31 target genes.

Keywords: two group comparison

overall_design: We used miRNA mimics to over-express mir-31, originally found under-expressed in OvCa.  After 48 hours of mimic treatment, we profiled for gene expression both cells with mir-31 knockup and cells with mimic control (having minimal sequence identity with all human miRNAs).

first: Preethi

first: Matt

first: Ankur

last: Nagaraja

last: Fountain


title: Gene expression changes underlying initial cellular and molecular responses to MAMPs in Arabidopsis mesophyll cells

first: Jen

last: Sheen


title: Identification of early flg22 responsive genes in Arabidopsis mesophyll cells

summary:
The goal of this experiment was to identify the early responsive genes activated by the 22 amino acid peptide of bacterial flagellin (flg22) in Arabidopsis mesophyll cells that are involved in the initial responses important for plant innate immunity.
We used the microarrays to detail the global program of gene expression underlying intial cellular and molecular responses to microbial associated molecualr patterns (MAMPs).

overall_design: Arabidopsis mesophyll protoplasts were treated with 100 nM flg22 for 30 min and 60 min.  Transcript profiles were analyzed and compared between control and treated cells to identify early flg22 responsive genes.

first: Horim

last: Lee

first: Matthew

last: McCormack


title: Genome-Wide Analysis Revealed the Complex Regulatory Network of Brassinosteroid Effects in Photomorphogenesis

city: Shang Hai

first: Li

last: Song

address: FengLin Road

country: China

institute: SIPPE

summary: Light and brassinosteroids (BRs) have been proved to be crucial in regulating plant growth and development, however, the mechanism of how they synergistically function is still largely unknown. To explore the underlying mechanisms in photomorphogenesis, genome-wide analyses were carried out through examining the gene expressions of the dark-grown WT or BR biosynthesis-defective mutant det2 seedlings in presence of light stimuli, or exogenous Brassinolide (BL). Results showed that BR deficiency stimulates, while BL treatment suppresses, the expressions of light responsive genes and photomorphogenesis, revealing the negative effects of BR in photomorphogenesis. This is consistent with that genes involved in cell wall modification and cellular metabolism were specifically modulated by BL during dark-light transition, and altered expressions of genes related to energy utilization. Further analysis revealed that hormone biosynthesis and signaling related genes, especially those of auxin, were altered under BL treatment or light stimuli, indicating that BR may modulate photomorphogenesis through synergetic regulation with other hormones. Additionally, suppressed ubiquitin-cycle pathway during light-dark transition hinted the presence of a complicated network among light, hormone and protein degradation. The study provides the direct evidence of BR effects in photomorphogenesis and identified the genes involved in BR and light signaling pathway, which will help to elucidate the molecular mechanism of plant photomorphogenesis.

overall_design:
In order to study how BR involves in photomorphogenesis, dark-grown wild-type or BR- deficient mutant det2 seedlings were treated with BL or light, gene expression pattern analysis confirmed that BR deficiency specifically induces, while BL treatment suppresses, the expression of photosynthesis and light responsive genes. Interplay of BR and other hormones play important roles in dark-light transition and photomorphogenesis.

CEL files for the wildtype samples are lost.
14 samples were analysised and including repeats.

first: Xiao-Yi

last: Zhou

first: Liang-Jiao

last: Xue

first: Xi

last: Yang

first: Hong-wei


title: Gene expression analyses of ovarian clear cell cancer cell lines

summary:
A variety of human cancers demonstrate alterations in microRNA expression.  We hypothesized that regulatory defects in microRNAs play a central early role in organizing the molecular changes involved in ovarian cancer (OvCa).  Using both gene arrays and deep sequencing, we comprehensively profiled mRNA and microRNA expression, respectively, in human clear cell epithelial OvCa cell lines and short-term primary cultures of normal ovarian surface epithelium.  We expected that over-expression of a specific microRNA would lead to lower expression of its mRNA targets, and under-expression of a specific microRNA would lead to higher expression of its target genes.  Using our expression data in conjunction with established in silico algorithms, we found putative microRNA:mRNA functional pairs.

Keywords: two group comparison; gene expression profiling

overall_design: We generated gene expression profiles of a panel of ten OvCa clear cell cell lines, along with six independent normal ovarian surface epithelium (NOSE) cultures.


title: Gene expression analyses of mir-100 overexpression in ovarian clear cell cancer cell line

summary:
A variety of human cancers demonstrate alterations in microRNA expression.  We hypothesized that regulatory defects in microRNAs play a central early role in organizing the molecular changes involved in ovarian cancer (OvCa).  Using both gene arrays and deep sequencing, we comprehensively profiled mRNA and microRNA expression, respectively, in human clear cell epithelial OvCa cell lines and short-term primary cultures of normal ovarian surface epithelium.  We expected that over-expression of a specific microRNA would lead to lower expression of its mRNA targets, and under-expression of a specific microRNA would lead to higher expression of its target genes.  Using our expression data in conjunction with established in silico algorithms, we found putative microRNA:mRNA functional pairs.  Furthermore, gene expression profiles were taken of clear cell cultures having functional knockdown or over-expression of specific microRNAs of interest.  Knockdown of mir-100 (found under-expressed in clear cell OvCa) resulted in down-regulation in vitro of a significant number of the in silico predicted mir-100 target genes that were normally over-expressed in OvCa.

Keywords: two group comparison; gene expression profiling

overall_design: We used miRNA mimics to overexpress mir-100, originally found under-expressed in OvCa (fold>100).  After 48 hours of mimic treatment, we profiled gene expression for both cells with mir-100 knockup and cells with mimic control (having minimal sequence identity with all human miRNAs).


title: Gene expression analyses of putative miRNA targets in ovarian clear cell cancer cell lines


title: Gene expression analyses of mir-22 overexpression in ovarian clear cell cancer cell line

summary:
A variety of human cancers demonstrate alterations in microRNA expression.  We hypothesized that regulatory defects in microRNAs play a central early role in organizing the molecular changes involved in ovarian cancer (OvCa).  Using both gene arrays and deep sequencing, we comprehensively profiled mRNA and microRNA expression, respectively, in human clear cell epithelial OvCa cell lines and short-term primary cultures of normal ovarian surface epithelium.  We expected that over-expression of a specific microRNA would lead to lower expression of its mRNA targets, and under-expression of a specific microRNA would lead to higher expression of its target genes.  Using our expression data in conjunction with established in silico algorithms, we found putative microRNA:mRNA functional pairs.  Furthermore, gene expression profiles were taken of clear cell cultures having functional knockdown or over-expression of specific microRNAs of interest.  Knockdown of mir-22 (found under-expressed in clear cell OvCa) resulted in down-regulation in vitro of a significant number of the in silico predicted mir-22 target genes that were normally over-expressed in OvCa.

Keywords: two group comparison; gene expression profiling

overall_design: We used miRNA mimics to over-express mir-22, originally found under-expressed in OvCa (fold>6).  After 48 hours of mimic treatment, we profiled for gene expression both cells with mir-22 knockup and cells with mimic control (having minimal sequence identity with all human miRNAs).


title: Gene expression analyses of mir-30a knockdown in ovarian clear cell cancer cell line

summary:
A variety of human cancers demonstrate alterations in microRNA expression.  We hypothesized that regulatory defects in microRNAs play a central early role in organizing the molecular changes involved in ovarian cancer (OvCa).  Using both gene arrays and deep sequencing, we comprehensively profiled mRNA and microRNA expression, respectively, in human clear cell epithelial OvCa cell lines and short-term primary cultures of normal ovarian surface epithelium.  We expected that over-expression of a specific microRNA would lead to lower expression of its mRNA targets, and under-expression of a specific microRNA would lead to higher expression of its target genes.  Using our expression data in conjunction with established in silico algorithms, we found putative microRNA:mRNA functional pairs.  Furthermore, gene expression profiles were taken of clear cell cultures having functional knockdown or over-expression of specific microRNAs of interest.  Knockdown of mir-30a (found over-expressed in clear cell OvCa) resulted in up-regulation in vitro of a significant number of the in silico predicted mir-30a target genes that were normally under-expressed in OvCa.

Keywords: two group comparison; gene expression profiling

overall_design: We used miRNA mimics to knockdown expression of mir-30a, which was over-expressed (fold>8) in OvCa clear cell cultures versus NOSE, using the clear cell line OVSAYO.  After 48 hours of mimic treatment, we profiled for gene expression both cells with mir-30a knockdown and cells with mimic control (having minimal sequence identity with all human miRNAs).


title: Multi-level Support Vector Regression analysis to identify condition-specific regulatory networks

status: Public on Mar 10 2010

city: Arlington

middle: Lily

last: Chen

state: VA

address: 4300 Wilson Blvd., Suite 750

department: The Bradley Department of Electrical and Computer Engineering

institute: Virginia Tech

summary:
The identification of gene regulatory modules is an important yet challenging problem in computational biology. While many computational methods have been proposed to identify regulatory modules, their initial  success is largely compromised by a high rate of false positives, especially when applied to human cancer studies. New strategies are needed for reliable regulatory module identification.
We present a new approach, namely multi-level support vector regression (ml-SVR), to systematically identify conditionspecific regulatory modules. The approach is built upon a multi-level analysis strategy designed for suppressing false positive predictions. With this strategy, a regulatory module becomes ever more significant as more relevant gene sets are formed at finer levels. At each level, a two-stage support vector regression (SVR) method is utilized to help reduce false positive predictions by integrating binding motif information and gene expression data; a significant analysis procedure is followed to assess the significance of each regulatory module. We applied our method to breast cancer cell line data to identify condition-specific regulatory modules associated with estrogen treatment. Experimental results show that our method can identify biologically meaningful regulatory modules related to estrogen signaling and action in breast cancer.

overall_design: Three independent total RNA samples were extracted for each cell line (MCF-7 and MCF-7-stripped) and the samples were arrayed using Affymetrix GeneChip HG-U133A. MCF-7-stripped denotes estrogen-deprived MCF-7 human breast cancer cells, which were grown in the absence of estrogen for 96 hours. We analyzed the enriched motifs and their targets for the genes significantly down-regulated in MCF-7-stripped cells as compared to MCF-7 cells.

first: Jianhua

last: Xuan

first: Rebecca

last: Riggins

first: Yue

last: Wang

first: Eric

middle: P

last: Hoffman

first: Robert

last: Clarke


title: Expression data from Arabidopsis seed compartments at the bending coyledon stage

status: Public on Jan 27 2010

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California, Davis

summary: We collected bending-cotyledon seed compartments from 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing bending cotyledon stage embryos. For the purposes of this study we captured 6 compartments: embryo proper, mycropylar endosperm, cellularized peripherial endosperm, chalazal endosperm, chalazal seed coat and seed coat, in addition to serial sections encompasing the entire bending-cotyledon stage seed.

overall_design: Bending-cotyledon stage seed compartments were isolated using the LMD6000 system. Total RNA was amplified and hybridized with Affymetrix ATH1 Arabidopsis array for 14 samples (embryo proper, micropylar endosperm, peripherial endosperm, chalazal endosperm, chalazal seed coat, seed coat and whole seeds, 2 biological replicates each).

first: Ryan

last: Kirkbride

first: Mark

last: Belmonte

first: Jiong

last: Fei

first: Meryl

last: Hashimoto

first: Sandra

last: Stone

first: Julie

last: Pelletier

first: Chen

last: Cheng

last: Golberg


title: Identifying genetic profiles for functionally distinct clonal populations derived from the Detroit 562 cell line

status: Public on Jan 22 2010

city: Woolloongabba

first: Sarina

last: Cameron

state: QLD

address: Level 4, R wing, PA Hospital

institute: Diamantina Institute

summary: Single clones were isolated from the Detroit 562 cell line and implanted into NOD/SCID mice to determine whether clonal populations within one cell line had fuctionally distinct phenotypes, in the form of differing tumour initiating activity. From these data I found that different clonal populations had different tumour initiating activity, which lead to this investigation as to whether these functionally distinct populations were also genetically distinct.

overall_design: The different clonal populations were grown to confluence in culture, then harvested, counted and placed in trizol.

first: Gethin

last: Thomas

first: Ran

last: Duan

first: Paul

last: Leo

first: Ping

last: Zhang


title: Gene expression analysis of Drosophila melanogaster taste tissue

city: Berkeley

first: Peter

address: GL71 Koshland, UC-Berkeley

institute: UC-Berkeley

summary: To uncover novel molecules involved in taste detection, we performed a microarray-based screen for genes enriched in taste neurons.  Proboscis RNA from flies homozygous for a recessive poxn null mutation was compared to RNA from heterozygous controls.  Poxn mutants have a transformation of labellar gustatory chemosensory bristles into mechanosensory bristles and therefore lack most or all taste neurons.

overall_design: Proboscises of poxn70 homozygous mutant and poxn70 heterozygous mutant males (8-18 days post eclosure) were dissected, and total RNA was harvested in Trizol according to standard trizol protocol.  Samples for each microarray were prepared from 164-280 proboscises.  We performed 3 biological replicates for each genotype.

middle: S

first: Makoto

last: Hiroi

last: Ngai

first: Kristin

last: Scott


title: A transcriptional module initiates and maintains mesenchymal transformation in brain tumors [human data]

status: Public on Feb 12 2010

city: New York

first: Mariano

middle: Javier

last: Alvarez

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

summary: Using a novel combination of cellular-network reverse-engineering algorithms and experimental validation assays, we identified a transcriptional module, including six transcription factors that synergistically regulates the mesenchymal signature of malignant glioma. This is a poorly understood molecular phenotype, never observed in normal neural tissue. It represents the hallmark of tumor aggressiveness in high-grade glioma, and its upstream regulation is so far unknown. Overall, the newly discovered transcriptional module regulates >74% of the signature genes, while two of its transcription factors (C/EBPβ and Stat3) display features of initiators and master regulators of mesenchymal transformation. Ectopic co-expression of C/EBPβ and Stat3 is sufficient to reprogram neural stem cells along the aberrant mesenchymal lineage, while simultaneously suppressing differentiation along the default neural lineages (neuronal and glial). Conversely, silencing the two transcription factors in human glioma cell lines and glioblastoma-derived tumor initiating cells leads to collapse of the mesenchymal signature with corresponding loss of tumor aggressiveness in vitro and in immunodeficient mice after intracranial injection. In human tumor samples, combined expression of C/EBPβ and Stat3 correlates with mesenchymal differentiation of primary glioma and is a predictor of poor clinical outcome. Taken together, these results reveal that activation of a small regulatory module – inferred from the accurate reconstruction of transcriptional networks – is necessary and sufficient to initiate and maintain an aberrant phenotypic state in eukaryotic cells.

overall_design: SNB19 human glioma cells and GBM-derived brain tumor initiating cells were transduced with STAT3 and CEBPB shRNA lentiviral vectors.

first: Maria

last: Carro

first: Wei

middle: K

last: Lim

first: Robert

last: Bollo

first: Xudong

last: Zhao

first: Evan

middle: Y

last: Snyder

first: Erik

last: Sulman

first: Sandrine

last: Anne

first: Fiona

last: Doetsch

first: Howard

last: Colman

first: Anna

last: Lasorella

first: Ken

last: Aldape

first: Andrea

last: Califano

first: Antonio

last: Iavarone


title: Rhabdoid Tumor: Gene Expression Clues to Pathogenesis and Potential Therapeutic Targets

status: Public on Feb 28 2010

first: Elizabeth

last: Perlman

address: 2373 North Lincoln Avenue, Room A.204

department: Pathology

institute: Northwestern University/Children's Memorial Hospital

summary:
Rhabdoid tumors (RT) are aggressive tumors characterized by genetic loss of SMARCB1 (SNF5, INI-1), a component of the SWI/SNF chromatin remodeling complex.  No effective treatment is currently available.  This study seeks to shed light on the SMARCB1-mediated pathogenesis of RT and to discover potential therapeutic targets.  Global gene expression of 10 RT was compared with 12 cellular mesoblastic nephromas, 16 clear cell sarcomas of the kidney, and 15 Wilms tumors.  114 top genes were differentially expressed in RT (p<0.001, fold change >2 or <0.5).  Among these were down-regulation of SMARCB1 and genes previously associated with SMARCB1 (ATP1B1, PTN, DOCK4, NQO1, PLOD1, PTP4A2, PTPRK).  28/114 top differentially expressed genes were involved with neural or neural crest development and were all sharply down-regulated.  This was confirmed by Gene Set Enrichment Analysis (GSEA). Neural and neural crest stem cell marker proteins SOX10, ID3, CD133 and Musashi were negative by immunohistochemistry, whereas Nestin was positive. Decreased expression of CDKN1A, CDKN1B, CDKN1C, CDKN2A, and CCND1 was identified, while MYC-C was upregulated.  GSEA of independent gene sets associated with bivalent histone modification and polycomb group targets in embryonic stem cells demonstrated significant negative enrichment in RT.   Several differentially expressed genes were associated with tumor suppression, invasion and metastasis, including SPP1 (osteopontin), COL18A1 (endostatin), PTPRK, and DOCK4.   We conclude that RTs arise within early progenitor cells during a critical developmental window in which loss of SMARCB1 directly results in repression of neural development, loss of cyclin dependent kinase inhibition, and trithorax/polycomb dysregulation.

Keywords: Gene expression; rhabdoid tumor; pediatric renal tumors; neural crest

overall_design:
The goal of this study is to identify genetic pathways that will clarify the nature of RT and enable the identification of therapeutic targets.

Experimental Design:
Frozen tissue samples were obtained from the Renal Tumor Bank of the Children's Oncology Group (COG).  A total of 53 tumors were hybridized to Affymetrix U133A arrays and analyzed including 10 RT, 12 cellular mesoblastic nephromas (CMN), also known as infantile fibrosarcomas, 16 clear cell sarcomas of the kidney (CCSK) and 15 Wilms tumors (WT).

Quality control steps taken:
1. Samples were snap frozen immediately following surgery and were mailed on dry ice to the Tumor Bank and retained at -80°C.
2. Frozen sections were evaluated histologically and tumors with less than 80% viable tumor cellularity were excluded.
3. Array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches.
4. Samples for which the 3'/5' ratios for GAPDH were greater than 3.4 were excluded.
5. The BioB spike controls were confirmed as present 90% of the time; BioC, BioD and cre were confirmed as increasing intensity in all samples.
6. When scaled to a target intensity of 2500, scaling factors were between 13 and 52; background levels were 34-115: Raw Q values were 1.3-3.7 and mean intensities were within acceptable limits.
7. The range of percent present calls was from 30% to 52%.

Statistical Analysis:
Positional-dependent-nearest-neighbor model (PDNN) software was used to translate the scanned images into expression analysis files and to normalize the data across all arrays.
To establish a broad list of probesets containing the majority of genes significant in the pathogenesis of RT, the expression of 10 RT was compared with the 43 other tumor types combined (non-RT) using the two-sample t-test, resulting in 2921 probesets with p-value <0.005 and false discovery rate of <1%. This data is provided in the attached supplementary file 'Supplemental Table 1'.  To define probesets more uniquely expressed in RT, the gene expression of RT was compared with each of the other tumor types separately (CCSK, CMN, and WT) using the two-sample t-test, and genes present in each one of the resulting four comparisons (RT vs. CCSK, RT vs. CMN, RT vs. WT and RT vs non-RT) with a p-value of <0.001 are provided in the attached supplementary file 'Supplemental Table 2'. Lastly, the 766 genes differentially expressed between RT and non-RT (p<0.0001) were analyzed in PANTHER (Protein ANalysis THrough Evolutionary Relationships), and those groups within the biologic process category over-represented with a Bonferoni corrected p value<0.05 are listed in the attached file labelled 'Supplemental Table 3'.

first: Samantha

last: Gadd

first: Simone

last: Sredni

first: Chiang-Ching

last: Huang


title: Expression data from Col-0 and pil5 imbibed seeds after far-red or far-red/red light irradiation.

status: Public on Jan 12 2010

city: Daejeon

first: Giltsu

last: Choi

address: 335 Gwahangno

country: South Korea

institute: KAIST

summary:
PIL5 is a key negative regulator of phytochrome mediated seed germination and PIL5 protein is degraded by red light irradiation through phytochrome. The microarray aimed to find various red light-regulated genes and PIL5-regulated genes in the imbibed seeds.

Keywords: genetic modification

overall_design: Col-0 and pil5 seeds were irradiated by far-red light or far-red/red light and then, incubated in the dark for 12 hours. Total three biological replicates were used for the microarray.


title: Widespread regulation of gene expression by the histone acetyltransferase dTip60

status: Public on Jan 19 2010

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

summary: We used microarrays to detail the global gene expression changes following RNAi knock-down of dTip60 in Drosophila SL2 cells

overall_design: We compared SL2 cells treated with dTip60-RNAi with SL2 cells mock-treated with eGFP-RNAi to determine global gene expression changes by microarray analysis

first: L

first: C

last: Schirling


title: Gene expression in a Drosophila model of mitochondrial disease

city: Sevilla

first: Daniel Jose

last: Moreno Fernandez-Ayala

address: Carretera de Utrera, Km. 1

institute: Universidad Pablo de Olavide

summary:
Background: A point mutation in the Drosophila gene technical knockout (tko), encoding mitoribosomal protein S12, provokes a phenotype of respiratory chain deficiency, developmental delay and neurological abnormalities similar to those presented in many human mitochondrial disorders, as well as defective courtship behaviour.
Results: Transcriptome-wide analysis of gene expression in tko25t mutant flies revealed systematic, compensatory changes in expression of genes connected with metabolism, including upregulation of lactate dehydrogenase and of many genes involved in the catabolism of fats and proteins, the TCA cycle and anaplerotic pathways feeding into it.  Gut-specific enzymes involved in the primary mobilization of dietary fat and protein, as well as a number of transport functions, were strongly upregulated, consistent with the idea that OXPHOS dysfunction is perceived physiologically as a starvation for particular biomolecules.  Many stress-response genes were also induced.  Other changes may reflect a signature of developmental delay.  There was also down-regulation of genes connected with reproduction, including gametogenesis, especially in females, and courtship behaviour in males. This might represent a programmed response to a mitochondrially generated starvation signal.  Although human sexual behaviour is not known to respond to mitochondrial dysfunction, the underlying signaling pathway, if conserved, could influence many physiological processes in response to nutritional stress.  Transcriptomic analysis suggested the possible involvement of the Akt1/sgg signaling pathway(s).
Conclusions: The transformation of metabolism in response to mitochondrial dysfunction, including digestive and absorptive functions, gives important clues as to how novel therapeutic strategies for mitochondrial disorders might be developed.
Keywords: mutant analysis

overall_design:
Crosses and maintenance: Inbreeding under stressful conditions inevitably results in the selection of compensatory alleles of many genes. In order to avoid such issues, and thus determine the global effects on gene expression of the tko25t mutation in a truly unselected and 'wild-type' background, we outbred tko25t over more than 10 generations by back-crossing to each of two commonly used wild-type strains, Canton S and Oregon R. Subsequent to this backcrossing, tko25t was maintained in each background using a balancer chromosome. These stocks were then used to generate a tko25t mutant F1 generation, by crossing virgin Canton S tko25t homozygous mutant females with Oregon R tko25t males. For comparison, we generated otherwise isogenic wild-type F1 progeny by crossing virgin Canton S wild-type females with Oregon R wild-type males.
Samples: Both tko25t and wild-type Drosophila adult flies of both sexes were collected and aged to 1 day old prior to RNA extraction and hybridization on Affymetrix microarrays. We extracted RNA from 3 independent such crosses.
Comparative analysis: Data analysis for each gene in the array compared each tko25t mutant RNA isolate with each wild-type RNA isolate from flies of the given sex, generating 9 comparative measurements, over which the statistical analysis was performed.

first: Daniel

last: Fernández-Ayala

first: Shanjun

last: Chen

first: Esko

last: Kemppainen

first: Kevin

last: O’Dell

last: Jacobs


title: Arabidopsis mutants treated with flg22, Alternaria brassicicola, Methyl jasmonate and Pst DC3000 bacteria

status: Public on Jan 15 2010

city: Norwich

last: MacLean

address: Colney Lane

department: Bioinformatics

institute: The Sainsbury Laboratory

summary:
Gibberellin (GA) promotes plant growth by destabilizing DELLA proteins. DELLA proteins integrate multiple hormonal and environmental stress responses. We investigated the role of GA and DELLA proteins in plant defence.
We used microarrays to detail the global programme of gene expression controlled by DELLA proteins and identified distinct classes of differentially regulated genes in response to pathogens, hormones or pathogen elicitors.

overall_design: Five weeks old short day grown Arabidopsis leaf discs were used to treat with flg22 and samples were collected after 1 hour and 2 hour time points. For Alternaria brassicicola, five weeks old plants were drop inoculated with 4x 5µl droplets of Alternaria brassicicola spores (5x105 spores/ml) and samples were collected 3 days post inoculation. Five weeks old plants were infiltrated with Pst DC3000 (2x105cfu/ml) bacteria and samples were collected after 12 hours post infiltration. For methyl jasmonate treatments, five weeks old plants were sprayed with 10µM Methyl Jasmonate solution, covered with plastic bags and samples were collected after one hour.

first: Rajendra

last: Bari

first: Dan

first: Jonathan

last: Jones


title: Comparing epithelial and mesenchymal-like subsets within head and neck squamous cell carcinoma cell lines

status: Public on Jan 05 2010

city: Philadelphia

first: Gao

last: Zhang

state: PA

address: 3601 SPRUCE ST

department: Molecular and Cellular Oncogenesis Program

institute: Wistar Institute

summary: Segregating head and neck squamous cell carcinoma lines on the basis of high or low surface E-cadherin expression defines subpopulations within each line with distinctive epithelial and mesenchymal-like phenotypes.

overall_design:
SCC9 and OCTT2 cell lines were each sorted by flow cytometry into E-cadherin high and low expressing subpopulations and processed for hybridization to Illumina gene expression array chips. Expression intensities were calculated and normalized for each gene probed on the array for all hybridizations using illumina Beadstudio#3 software. Microarray analyses were subsequently performed using Bioconductor software to identify genes differentially-expressed between E-cadherin high and and E-cadherin low subsets in SCC9 and OCTT2 cells.

GEO staff have requested, but not yet received, the normalized data described in this submission.

first: Devraj

last: Basu

first: Thierry

last: Nguyen


title: H2A.Z - Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis

status: Public on Jan 08 2010

first: Vinod

last: Kumar

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

summary:
We isolated mutants in Arabidopsis with enhanced ambient temperature response. Microarray analysis was performed to understand the extent to which ambient temperature transcriptome is perturbed in the mutants in comparison with the WT at non inductive 12 ºC and after shift to inductive 27 ºC for 2 h and 24 h.
We performed global transcript profiling to understand the regulation of of gene expression underlying ambient temperature response.

overall_design: Sterilized wild type Arabidopsis Col-0 as well as the arp6-10 mutant seeds were plated on half-strength MS plates without sugar. Plates were incubated at 4 ºC in dark  for 48 hours before transfering to 20 ºC  with light. 5 day old seedlings were transfered to 12 ºC incubaor with continuous light for 3 days befroe shifting to 27 ºC. Samples (Whole seedlings) were collected before shifting (0 h) and 2 h and 24 h after shifting to 27 ºC by immediately freezing in liquid nitrogen.

first: S

middle: V

first: Philip

middle: A

last: Wigge


title: Gene expression in aerial parts of rice-Arabidopsis Os-LBD37 FOX plants

status: Public on Dec 27 2009

city: Yokohama

first: Miyako

last: Kusano

state: Kanagawa

address: 1-7-22, Suehiro, Tsurumi

country: Japan

institute: RIKEN CSRS

summary: Aerial parts of the rice-Arabidopsis FOX (Full-length cDNA overexpressor) lines K16331 and K19624 harboring the rice FL cDNA of LBD37 (Os-LBD37) were analyzed. LBD37 belongs to the plant- specific LOB- (Lateral Organ Boundary) domain family proteins first characterized in Arabidopsis. Results point towards an involvement of the rice LBD37 ortholog of Arabidopsis in nitrogen metabolism- related processes.

overall_design:
K16331 (T2) and empty vector control plants (T2) were grown for 18 days on solid MS- medium supplemented with 20mg/l Hygromycin. For each hybridization on Affymetrix microarrays, 2 independent plants for K16331 were used.
Homozygote K19624 (T3) and empty vector control plants (T3) were grown for 18 days on solid MS- medium. For each hybridization on Affymetrix microarrays, 1 plant was used.

first: Doris

last: Albinsky

first: Atsushi

last: Fukushima

first: Naomi

last: Hayashi


title: Gene Expression Circulating B Lymphocytes for Smoking Females

status: Public on Dec 25 2009

city: Xi'an

first: Feng

last: Pan

state: Shaanxi

address: Xian Ning West Road 28

department: School of life science and technology

institute: Xi'an Jiaotong University

summary:
B cells were found to be directly associated with the onset and development of many smoking-induced diseases. However, the in vivo molecular response of B cells underlying the female cigarette smoking remains unknown.
Using the genome-wide Affymetrix HG-133A GeneChip® microarray, we compared the gene expression profiles of peripheral circulating B cells between 39 smoking and 40 non-smoking healthy US white females.

overall_design: B cells were isolated from 70 ml of whole blood from each subject using B cell positive isolation method (Dynabeads CD19,Pan B) from Invitrogen Life Technologies Dynal Biotech Inc,CA. Total RNA was extracted from B cells using Qiagen RNeasy Mini Kit. A total of 4ug total RNA was used to produced targets for each subject according to standard Affymetrix procedures. Hybridization was made for each subject. Multiple analytic approaches including mas5.0 algorithm (Affymetrix, Santa Clara, CA, USA), RMA (Robust Multiarray Algorithm), GCRMA (the improved GC-content adjusted RMA), and dChip were used for converting and normalizing our raw probe data to gene expression values Comparison was performed between smoking and non-smoking groups using t-test under Benjamini and Hochberg (BH) procedure mutiple-testing adjustment.


title: Involvement of the rice LBD37 (OsLBD37) ortholog of Arabidopsis in nitrogen metabolism- and senescence-related processes

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

sample_organism:
Arabidopsis thaliana
Oryza sativa

platform_organism:
Arabidopsis thaliana
Oryza sativa

overall_design: Refer to individual Series


title: An mRNA/3' UTR-directed primary piRNA pathway in Drosophila ovarian somatic cells

status: Public on Jan 04 2010

first: Nicolas

last: Robine

address: 430, East 67th Street, RRL 517

department: Developmental Biology

institute: Sloan-Kettering Institute

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Piwi-interacting RNAs (piRNAs) are ~24-30 nucleotide regulatory RNAs that are abundantly expressed in gonads. The most well-understood piRNAs mediate post-transcriptional defense against transposable elements (TEs), and derive from sense or antisense strands as a consequence of "ping-pong" amplification of complementary sequences of active TEs and piRNA master control transcripts. Another class of piRNAs, such as those expressed in pachytene testis, derive from large intergenic clusters that are strictly single-stranded. Here, we report a third substrate that generates abundant primary piRNAs. In somatic follicle cells of Drosophila ovaries, we cloned >1 million piRNAs from thousands of messenger RNAs, and these were quite preferentially derived from 3' untranslated regions.  This segregation implies a competition between the translation machinery and primary piRNA biogenesis machinery for mRNA access.

overall_design: 3 replicates.

first: Sudha

last: Balla

first: Nelson

last: Lau

first: Eric

middle: C

last: Lai


title: Gene Expression in Human Lung Type II Cells

status: Public on Dec 30 2009

city: San Francisco

middle: L

last: Ballard

address: 513 Parnassus St

department: Neonatology

institute: UCSF

summary:
Normal lung function relies on mature function of alveolar type II cels, which have numerous functions including to regulate ion and fluid flux, produce immune molecules, and synthesize and secrete surfactant to stabilize air spaces.  Differentiation of type II cells from precursor epithelial cells is accelerated by exposure of cultured cells to glucocorticoid and cAMP.
In these studies we used DNA microarray analysis to identify genes of both fetal and adult type II cells that are regulated by glucocorticoid plus cAMP.

overall_design:
In the first series of experiments we isolated epithelial cells from fetal human lung and cultured cells for 5 days with or without hormone treatment (dexamethasone plus 8-Br-cAMP plus isobutylmethylxanthine, DCI) and then performed DNA microarray analysis.
In the second series of experiments, we isolated type II cells from adult human postmortem lung and cultured cells for 5 days with or without DCI and performed DNA microarray analysis.


title: Transcriptional program of terminal granulocytic differentation

status: Public on Dec 19 2009

city: Princeton

first: Troels

middle: Torben

last: Marstrand

state: NJ

address: Lewis-Sigler Institute Princeton University

institute: Princeton University

summary: To characterize the transcriptional program that governs terminal granulocytic differentation in vivo, we performed comprehensive microarray analysis of human bone marrow population highly enriched for promyelocytes, myelocytes / metamyelocytes and neotrophils.

overall_design: Bone marrow and peripheral blood samples were collected from healthy individuals in parallel. Cell populations representing successive stages of terminal granulocytic differentation were isolated from human bone marrow samples by 2-layer density gradient centrifugation, neutrophils were collected from peripheral blood using 1-layer density gradient centrifugation. All populations were depleted of nongranulocytic cells by immunomagnetic sorting.

first: Kim

last: Theilgaard-Monch


title: Drosophila Duplication 20091218

status: Public on Dec 23 2009

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

summary: D. yakuba, D. simulans, and D. melanogaster female gDNA hybridized with D. melanogaster male gDNA to assess aCGH as a means of identification of duplicated genes

sample_organism:
Drosophila melanogaster
Drosophila simulans
Drosophila yakuba

overall_design: 6 D. melanogaster female vs D. melanogaster male hybs, 6 D. simulans female vs D. melanogaster male hybs, and 4 D. yakuba female vs D. melanogaster male hybs, all with balanced dye swaps

first: Renn

last: Suzy


title: An EGFR autocrine loop encodes a slow-reacting but dominant mode of mechanotransduction in a polarized epithelium

status: Public on Dec 16 2009

city: Boston

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary:
Normal human bronchial epithelial cells were studied under four different conditions: control, pressure 30 cmH2O, AG1478 (1 microM), and pressure plus AG1478 at 1, 3, and 8 hours, all in the absence of exogenous EGF.

Keywords: Normal human bronchial epithelial cells.

overall_design: Time series under 4 different stimuli with no replicate measurements.

first: Nikola

last: Kojic

first: Daniel

last: Tschumperlin


title: A combinatorial Interplay Among the ACC Synthase Isoforms Regulates Ethylene Biosynthesis in Arabidopsis thaliana

status: Public on Dec 15 2009

city: Albany

first: Atsunari

last: Tsuchisaka

address: 800 Buchanan St.

department: Plant Gene Expression Center

institute: University of California, Berkeley / USDA

summary:
ACC Synthase (ACS) is the key regulatory enzyme in the ethylene biosynthesis in plants. It catalyzes the conversion of s-adenosylmethionine (SAM) to 1-aminocyclopropane-1-carboxylic acid (ACC), the precursor of ethylene. Arabidopsis has nine ACS genes. The goal of the project is to inactivate each gene by insertional mutagenesis and amiRNA technology and eventually construct a null ACS mutant. We have been recently able to achieve this goal. Furthermore, we wanted to know how inactivation of individual ACS genes affects global gene expression.

Keywords: ACS mutant comprrison; global gene expression.

overall_design: Triplicate samples of 10-day light grown seedling from each ACS mutant was used for microarray analysis.

first: Guixia

last: Yu

first: Athanasios

last: Theologis


title: Genome-wide analysis of gene expression in colon and brain during the suckling period.

status: Public on Dec 18 2009

city: Lausanne

first: Peter

middle: I

last: Duncan

address: Vers-chez-les-Blanc

department: Nutrition & Health

institute: Nestlé Research Center

summary: Gene expression was analysed in the colon and brain of normal rat pups from late prenatal through early postnatal development. Tissue was isolated from pups one day prior to the anticipated date of birth and throughout the suckling period until the end of weaning.

overall_design:
Total RNA isolated from colon or brain of pups prior to birth (embryonic day 21) and on postnatal days 1, 2, 3, 5, 7, 10, 15, 22. 6 replicates per time point.
'Colon_Embryo_Day21_rep1' has been excluded from the analysis

first: Norbert

last: Sprenger


title: Biological function of Pip3

status: Public on Dec 10 2009

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary: Ralstonia solanacearum is the causal agent of bacterial wilt. Arabidopsis thaliana monogenic resistance to the strain GMI1000 is conferred by the RRS1-R gene, present in the resistant ecotype ND-1 and absent in the susceptible ecotype Col-0. The corresponding protein is recognized by the avirulence protein PopP2 of R. solanacearum. In order to identify the plant proteins involved in the PopP2/RRS1-R perception complex, the screening of a root cDNA library in yeast was performed using PopP2 as bait. One interactor found was called Pip3, and we would like to better understand its biological function. Thereby we choose to compare two RNAi lines with their wild type Nd-1 background, and one KO line with its wild type Col-0 background. Also, two overexpressor lines will be compared with their wilt type Nd-1 background and two with their Col-0 background.

overall_design: 27 samples were used in this experiment.

first: Yves

last: Marco


title: Gene expression data from children diagnosed with ALL in vitro sensitive or resistant to prednisolone

city: Rotterdam

first: Ronald

last: Stam

address: Dr. Molewaterplein 60

institute: Erasmus MC - Sophia Children's Hospital

summary:
Although the prognosis for childhood Acute Lymphoblastic Leukemia (ALL) in general has improved tremendously over the last decades, the survival chances for infants (<1 year of age) with ALL remains poor.
A major obstacle hampering successful treatment results in infant ALL is cellular resistance to several drugs currently used in the treatment of ALL, especially to prednisolone (or prednisone). Therefore we set out to search for genes differentially expressed between from infant (children <1 year of age) and non-infant (children >1 year of age) ALL samples either resistant or sensitive to prednisolone.

overall_design:
The in vitro prednisolone response in primary infant and non-infant ALL samples was determined by 4-day cytotoxicity (MTT) assays. Patient samples were characterized as either sensitive or resistant based on the LC50 value (i.e. the concentration of prednisolone lethal to 50% of the leukemic cells). Prednisolone sensitivity was defined by LC50 values <0.1 ug/mL prednisolone, and prednisolone resistance by LC50 values >150 ug/mL.
Samples showing intermediate in vitro prednisolone responses were excluded. In total 25 infant (<1 year of age) and 27 non-infant (>1 year of age) ALL samples were selected for RNA extraction and hybridization on Affymetrix HU133A microarrays. The obtained gene expression signatures were used to identify gene differentially expressed between prednisolone resistant and sensitive patients, in order to gain insights into the mechanism(s) underlying prednisolone resistance in infant and non-infant ALL.

first: Scott

last: Armstrong


title: DUO1 ectopic expression

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary: The experiment is designed to examine changes in gene expression upon ectopic expression of the germ line transcription factor DUO1 in Arabidopsis. Plants were transformed with the vector pMDC7DUO1, allowing induction of DUO1 by treatment with estradiol. T2 seedlings were selected on agar plates containing hygromycin for 12 days before seedlings were transferred to plates containing either 2 µM 17beta-estradiol (induced), or control plates containing DMSO (non-induced). Plants were grown for 6, 12 or 24 hours before harvesting. RNA was extracted using the RNAeasy kit from Qiagen. Each sample consists of 20 seedlings combined and all treatments have been conducted in triplicate.

overall_design: 18 samples were used in this experiment.

first: Lynette

last: Brownfield


title: Subsets of very low risk Wilms Tumors show distinctive gene expression, histologic, and clinical features

status: Public on Dec 22 2009

city: Chicago

first: Elizabeth

middle: J

last: Perlman

address: 2373 North Lincoln Avenue, Room A.204

institute: Children's Memorial Research Center

summary:
The goal of this study is to define biologically distinct subsets of Very Low Risk Wilms Tumors (VLRWT) using oligonucleotide arrays.

Description: 52 tumors from the original case:cohort of 600 tumors from NWTS-5 met the criteria for VLRWT.   Thirteen tumors were excluded for quality control reasons, resulting in 39 tumors for analysis.  Global gene expression analysis was performed on these 39 tumors. A total of 4,000 probesets representing the greatest variability according to coefficient of variation was utilized for hierarchical clustering, and three clusters were identified. Two subsets within VLRWT are identified that have pathogenetic and molecular differences and apparent differences in risk for relapse. If these predictors can be prospectively validated, this would enable future clinical stratification and broadening the definition of VLRWT.

Keywords: Classification by microarray analysis

overall_design:
Global gene expression analysis was performed on 39 tumors that met the criteria of VLRWT and passed quality control parameters in order to define biologically distinct subsets.

Hierarchical clustering  identified three tumor clusters (C1, C2 and C3). The top differentially expressed genes were identified by first filtering out probesets with a maximum expression of less than 6.5 in all 39 tumors. Using the remaining 14,452 probesets, the expression of each cluster was compared with the expression in the remaining tumors, and those genes with a p-value <0.00001 and positive or negative fold-change (FC) of greater than 2.5 were identified.  This resulted in 161 probesets from the comparison of C1 with C2+C3, 43 probesets from the comparison of C2 with C1+C3, and 71 probesets from the comparison of C3 with C1+C2.   The false discovery rates were 0.02%, 0.06% and 0.05% for C1, C2, and C3, respectively.  These three lists were combined, resulting in 239 probesets (161 genes) which are provided in Supplemental Table 1, linked below.

first: Samantha

last: Gadd


title: Acute ethanol exposure time-course in Drosophila melanogaster

city: Emeryville

first: Fred

last: Wolf

address: 5858 Horton St Suite 200

institute: Ernest Gallo Clinic and Research Center

summary: Increased ethanol intake, a major predictor for the development of alcohol use disorders, is facilitated by the development of tolerance to both the aversive and pleasurable effects of the drug. The molecular mechanisms underlying ethanol tolerance development are complex and are not yet well understood. To identify genetic mechanisms that contribute to ethanol tolerance, we examined the time course of gene expression changes elicited by a single sedating dose of ethanol in Drosophila.

overall_design: Microarray analysis of gene expression was carried out on the Berlin genetic background strain. For each treatment condition, three groups of 200 male flies each were treated identically and combined prior to RNA extraction; this design helped to minimize variations in ethanol dose and time of individual experiments. Treatment conditions were exposure to either humidified air (flow rate: 3.7 L/min) or ethanol vapor (saturated ethanol vapor diluted to 60% with humidified air to 3.7 L/min) for 30 min at 25°C in perforated 50 ml conical tubes. Treated flies were allowed to recover in standard culturing conditions (food containing vials kept at 25°C and 70% humidity) for 0, 30, 60, 90, 120, 180, and 210 min. Additionally, two independent groups of flies were given no treatment. Flies were quickly frozen and heads were isolated. RNA from the resulting 16 treatment conditions was hybridized to Affymetrix Drosophila 2.0 oligonucleotide microarray chips.

first: Eric

last: Kong

first: Lorien

last: Allouche

first: Paul

last: Chapot

first: Karen

last: Vranizan

first: Monica

last: Moore

first: Ulrike

last: Heberlein


title: Identifying Y candidate genes

summary: The circadian clock generates biological rhythms with a period of approximately 24 hours. Using microarray experiments, we have previously shown that approximately 16% of the Arabidopsis genome is regulated in a circadian manner (Edwards et al., 2006). Previous work from our lab in modelling the molecular oscillator of Arabidopsis introduced a hypothetical component Y into an evening loop of the clock gene network (Locke et al., 2005). GIGANTEA (GI) was suggested as a strong candidate for Y based on genetic evidence and its close matching of the expression profile predicted by the mathematical modelling. Recent experimental evidence suggests that GI may only partially account for the function of Y. Thus, we are undertaking a genomics approach to identify other candidate genes that match the predicted expression profile of Y. Samples were taken from wild type and lhy cca1 double mutant seedlings from 4 timepoints around the night to day transition (-15mins, +15mins, +30mins and +60mins) after 9 days of growth in 18:6 light dark cycles. We aim to identify genes showing the light induction response predicted for Y around dawn.

overall_design: 16 samples were used in this experiment.

first: Kieron

last: Edwards


title: Systemic responses to Pseudomonas syringae infection

summary: We used three different strains of Pseudomonas syringae pv tomato DC3000 to investigate systemic responses to infection in Arabidopsis and the development of SAR. Wildtype DC3000, the hrpA mutant and DC3000 carrying the avirulence gene avrRpm1 were syringe infiltrated into 4-week-old plants at a concentration of 10e8 cfu/ml. At least 5 leaves per plant were infiltrated and at least 10 plants were pooled for each sample. Systemic, uninfected tissue was then harvested at 8, 12 and 21h after inoculation. Three independent experiments were carried out to give three biological replicates for each timepoint.

first: William

last: Truman


title: Identification of circadian transcripts that are co-regulated with [Ca2+]cyt

summary:
Our aim is to identify circadian transcripts that are co-regulated with [Ca2+]cyt, with the eventual goal of identifying genetic regulators and targets for circadian oscillations of [Ca2+]cyt.  We have identified two conditions in which [Ca2+]cyt behaves differently to other circadian outputs.  1.  Treatment of plants with nicotinamide, a metabolic inhibitor of ADPR cyclase, abolishes the circadian oscillations of [Ca 2+]cyt. However, leaf movement, CCA1, LHY, TOC1 and CAB transcript abundance and CAB promoter activity are all rhythmic albeit with a longer period (Dodd et al., 2007). 2.  The toc1-1 mutant, which shortens the circadian period of all other rhythms tested, has no effect on the period of [Ca2+]cyt oscillations (Xu et al., 2007).  We will measure the circadian regulation of transcript abundance in wild type (C24), toc1-1 and nicotinamide (C24)-treated plants.
Method: Wild type (C24) and toc1-1 seeds were sown on 1/2MS 0.8% agar plates and imbibed at 4 C for 48 hours. Seedlings were grown in LD cycles of 12hL:12hD at 19 C for 11 days to entrain the oscillator.  Following transfer to LL at dawn on the 12th day, 50% of the wild type seedlings were dosed with 50 mM nicotinamide every 2 hours over the entire course of the experiment. Wild type, toc1-1 and nicotinamide-treated seedlings (approx. 100 for each sample, excluding roots) were harvested at 4 hour intervals from 49 to 93 hours in LL (12 time points covering the entire third and fourth circadian cycles). Two independent replicates of the whole experiment will be hybridised.

overall_design: 72 samples were used in this experiment.

first: Fiona

last: Robertson


title: Photoreceptor control of shoot meristem activity and leaf initiation

status: Public on Dec 05 2009

last: Nottingham Arabidopsis Stock Centre (NASC)

summary: When Arabidopsis seedlings are grown in the dark, their shoot meristem remains in a repressed state and does not develop leaves. The tight control of leaf development by light provides the opportunity to analyse a fundamental plant developmental process in its very early stages. We have observed that activation of photoreceptors in dark-grown seedlings leads to a rapid and dramatic increase in mitotic activity in and around the shoot meristem. Cotyledons also exhibit an induction of cell cycle activity by light, but this consists of endoreduplication and occurs later. Many other processes take place upon induction by light, including the development of the photosynthetic apparatus and the synthesis of sunscreens, but these processes are expected to take place in both the leaf primordia and the cotyledons. We have used this information to carry out a whole transcriptome analysis of shoot meristem activation and early stages of leaf development by light. For this we dissected the shoot apical regions from seedlings grown in the dark or 1, 2, 6, 24, 48 or 72 h after transfer to light. We also dissected cotyledons from equivalent seedlings grown in the dark or 1 or 6 h after transfer to light. From these samples we obtained RNA used for hybridisations against the ATH1 GenChip.

first: Enrique

last: Lopez-Juez


title: Inflammation and macrophage activation in adipose tissue of HIV-infected patients under antiretroviral treatment.

status: Public on Jan 09 2010

city: Paris

first: Véronique

last: Avettand-Fenoel

address: 22 rue Méchain

country: France

institute: INSERM U567

summary: We used microarrays to detail the global gene expression profile in subcutaneous adipose tissue between controls and HIV-infected patients under antiretroviral treatment.

overall_design: Subcutaneous adipose tissue biopsy from 7 HIV-infected patients and 6 control subjects were taken for RNA extraction and hybridization on Affymetrix microarrays.

first: Avettand-Fenoel

last: Veronique

first: Min

last: Kim

first: Barbara

last: Antuna-Puente

first: Emmanuelle

last: Meugnier

first: Jean-Philippe

last: Bastard


title: Microarray analysis of fdh1-3(avrB)

status: Public on Dec 04 2009

summary: To track gene expression profile in atgsnor1-3 mutant in response to Pst(avrB).

first: Byung-Wook

last: Yun


title: Temperature-controlled inhibition of phyB action

summary: It has been established that the frequently reported early flowering phenotype of the phyB mutant is very sensitive to small changes in ambient temperature (Halliday et al., 2003). A 6oC drop in temperature to 16oC is sufficient to abolish the pronounced early flowering phyB phenotype observed at 22oC. Using Affymetrix technology we will identify genes that are differentially regulated at 16oC and 22oC in a phyB-specific manner using phyB mutant and wild type seedlings.

first: Julia

last: Foreman


title: Transcript profiling of oestrogen treatment of primary human neuronal cell cultures

status: Public on Dec 01 2009

city: Stockholm

first: Linda

middle: Alexandra Csöregh

last: Nord

address: Karolinska University Hospital, Solna, C4:U1

department: Dept. of Women's and Children's Health

institute: Karolinska Institute

summary: The purpose of this experiment was to identify oestrogen regulated genes in human primary cell cultures of neuronal cells modelling the developing human nervous system. We were especially interested in genes involved in proliferation, differentiation and migration of neuronal cells and genes involved in or linked to neurodegenerative diseases. We have therefore assessed gene expression changes, using Affymetrix GeneChips (HG-U133A), of oestrogen treated human neuronal cell cultures.

overall_design: Primary neuronal cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. Procedures were approved by the local Ethics committee at the Karolinska University Hospital, Stockholm. A total of 28 tissue samples yielding 10 cell cultures were used in this experiment. Half of the cell cultures were treated with 2µM β-oestradiol the day after seeding. The duration of the oestrogen treatment was 7 days and the cells were harvested after 8 days of culturing for RNA extraction. Extracted RNA from untreated respectively oestrogen treated cell cultures were pooled yielding two samples, which were each hybridised to Affymetrix microarrys.

first: Eva

last: Andersson

first: Gabriel

last: Fried