title: Cohesin localisation along fission yeast chromosomes delineates conserved mechanisms of binding

status: Public on Dec 31 2008

first: Christine

middle: Katrin

last: Schmidt

address: 41 Library Drive, Bldg. 41, C619

department: LRBGE

institute: NCI (NIH)

summary: Cohesin holds sister chromatids together to enable their accurate segregation in mitosis. How, and where, cohesin binds to chromosomes are still poorly understood, and recent genome-wide surveys have revealed an apparent disparity between its chromosomal association patterns in different organisms. Here, we present the high-resolution analysis of cohesin localisation along fission yeast chromosomes. This reveals that several determinants, thought specific for distinct organisms, come together to shape the overall distribution. Cohesin is detected at chromosomal loading sites, characterised by the cohesin loader Mis4/Ssl3, in regions of strong transcriptional activity. Cohesin also responds to transcription by downstream translocation and accumulation at convergent transcriptional terminators surrounding the loading sites. As cells enter mitosis, a fraction of cohesin leaves chromosomes in a cleavage-independent reaction, while a substantial pool of cohesin dissociates when it is cleaved at anaphase onset. As a unique feature, centromeric cohesin spreads out onto chromosome arms during mitosis as the heterochromatin protein Swi6 dissociates from centromeres. Together, this allows us to suggest conserved mechanisms for chromosomal cohesin binding in eukaryotes.

overall_design:
After DNA replication in S phase, sister chromatids are held together by the cohesin complex. This allows DNA break repair by homologous recombination in G2 and bipolar attachment of the spindle to sister kinetochores in mitosis. At anaphase onset, sister chromatid cohesion is resolved to trigger chromosome segregation. Cohesin is an essential, conserved protein complex consisting of at least five subunits, Psm1, Psm3, Rad21, Psc3 and Pds5 in fission yeast (orthologs of budding yeast Smc1, Smc3, Scc1, Scc3 and Pds5, respectively). Chromatin immunoprecipitations against three different subunits of the cohesin complex, fused to two different epitope tags (Rad21-Pk9 -> GSM333001, Rad21-HA3 -> GSM333004, Psc3-Pk9 -> GSM333005 and Pds5-Pk9 -> GSM333006), yielded a reproducible binding pattern between approximately half of all available convergently transcribed gene pairs (in the following called convergent sites). The pattern was almost indistinguishable between exponentially growing cell populations (GSM333004, GSM333005, GSM333006) and cells arrested in G2 using the thermosensitive cdc25-22 mutation (GSM333001).
To understand why some, but not all, convergent sites are bound by cohesin, we analysed whether fission yeast cohesin responds to Pol II transcription by downstream translocation, like in budding yeast. As an example, we analysed cohesin at the convergent site between the rad21 and pof3 genes. rad21 expression is high during G1 and S phase, but low in G2. In cells arrested in G2 using the cdc25-22 allele, only a small cohesin peak was detectable that largely overlapped with the rad21 ORF (GSM333001). In contrast, in cells arrested in G1 using the cdc10-129 allele, the rad21 ORF was clear of cohesin and instead a large cohesin peak accumulated downstream of rad21 (GSM333007).
It has been suggested that transcriptional readthrough at convergent sites promotes double stranded RNA-dependent heterochromatin formation, which in turn underlies cohesin recruitment. We therefore tested whether the heterochromatin protein Swi6, thought to recruit cohesin, played a role in generating the observed cohesin pattern. We grew wild type and swi6Δ cells in synthetic medium lacking thiamine, conditions under which the nmt2 gene is transcribed at the nmt2/avn2 convergent site that has been studied as an example. In contrast to the prediction, the cohesin pattern along chromosome arms, including the nmt2/avn2 convergent site, remained unchanged in swi6Δ cells (GSM333008). We detected only small amounts of cohesin at the nmt2/avn2 convergent site, a class 1 convergent site following the above classification. At the centromeric repeats, cohesin levels were reduced in the absence of Swi6. These findings are consistent with previous reports implicating Swi6 in cohesin recruitment to centromeric heterochromatin, but not chromosome arms.
To compare cohesin’s pattern to its likely sites of chromosomal loading, we analysed the localisation of the cohesin loader subunits Mis4 and Ssl3. The two subunits showed a largely overlapping pattern of binding. Chromatin immunoprecipitation was performed against epitope-tagged Mis4-Pk9 (GSM333163) and Ssl3-Pk9 (GSM334196) from exponentially proliferating cells. As a control, cells without epitope-tagged protein were grown under identical conditions and processed in parallel for chromatin immunoprecipitation with an α-Pk antibody (GSM333230). The untagged control sample yielded trace amounts of immunoprecipitated DNA, which after amplification led to several strong peaks often in intergenic low complexity regions. Several of these peaks overlapped with Mis4/Ssl3 peaks, which were excluded from the analysis. Peaks in low complexity regions were not observed in chromatin immunoprecipitates of cohesin subunits (compare GSM333001).
In the search for an underlying determinant of Mis4/Ssl3 binding sites, we noticed a striking correlation with tRNA and ribosomal protein genes. Mis4/Ssl3 binding sites at tRNA genes overlapped with the binding profile of the Pol III transcription factor TFIIIC subunit Sfc6 (GSM334198), while at ribosomal protein genes it colocalised with the forkhead domain containing protein Fhl1 (GSM334307). Fhl1 is a possible fission yeast ortholog of the transcription factor Fhl1 that controls ribosomal protein gene expression in budding yeast. We found Sfc6 also associated with ribosomal protein genes, and Fhl1 with tRNA genes, though with weaker signal intensities. We do not currently know whether Sfc6 contributes to transcriptional control of ribosomal protein genes, and Fhl1 to that of tRNA genes, or whether the weaker levels of association may reflect indirect association, mediated by interactions between ribosomal protein and tRNA gene loci. Similar to budding yeast, Mis4/Ssl3 binding sites are also binding sites for the chromosomal condensin complex (GSM334197), which may mediate such interactions.
Having identified the binding sites of the Mis4/Ssl3 cohesin loader, we wanted to analyse its relationship with the cohesin distribution along chromosome arms. If Mis4/Ssl3 cohesin loading sites promote cohesin binding in their surrounding, deletion of a loading site should alter this pattern. To test this, we deleted a 489 bp sequence, containing two adjacent tRNA genes that form a Mis4/Ssl3 and cohesin binding site, on the left arm of chromosome 2. In response to the deletion, Mis4/Ssl3 binding to this locus disappeared (GSM334308). Cohesin was also no longer detected at this site (GSM334309), consistent with the notion that cohesin loading had been disrupted. However, the cohesin distribution at convergent sites surrounding the former loading site remained unchanged. This suggests that establishment of the cohesin pattern did not depend on a specific Mis4/Ssl3 binding site. Despite the tRNA deletion, residual Mis4/Ssl3 remained detectable in the vicinity of this site (GSM334308). Cohesin loading by Mis4/Ssl3 might therefore be less restricted to its peaks of binding than the pattern suggests. Alternatively, other determinants, e.g. gene orientation and their transcriptional activity, might define cohesin distribution at this locus.
We next addressed how cohesin on fission yeast chromosomes responds to loss of sister chromatid cohesion during mitosis and whether cohesin removal in mitosis affected certain regions of the chromosome more than others. In order to follow cohesin through mitosis, we arrested a cell population in G2 using the thermosensitive cdc25-22 mutation and released the culture into synchronous mitotic progression at permissive temperature.The cohesin pattern remained largely unchanged throughout G2, metaphase and anaphase, although the height of peaks along chromosome arms decreased. This suggests that cohesin is not removed from a subset of its binding sites during mitosis, but that its association among most binding sites was uniformly reduced. A noticeable change to the cohesin pattern during mitosis became apparent around centromeres. Over a region of approximately 50 kb surrounding the centromeres, cohesin appeared to spread along chromosome arms, showing little preference for convergent sites. The spreading started as cells entered metaphase (GSM334316) and became most pronounced during anaphase (GSM334317). We also observed a similar, although less pronounced, spreading around centromeres in cells arrested in G1 using the cdc10-129 thermosensitive mutation (GSM333007). This suggests that spreading of cohesin around centromeres is cell cycle stage specific.
Cohesin is enriched at the centromeric repeat regions (GSM333001), tethered by the heterochromatin protein Swi6, possibly after being loaded at core centromere sequences, where we observed strong Mis4/Ssl3 accumulation (GSM333163 & GSM334196). In mitosis, Swi6 levels are reduced after aurora B kinase-dependent phosphorylation of histone H3, and it reaccumulates as cells enter the subsequent S phase. To test whether loss of Swi6-dependent

middle: K

first: Neil

last: Brookes

first: Frank

last: Uhlmann


title: MMP1 and MMP7 as potential peripheral blood biomarkers in Idiopathic Pulmonary Fibrosis

status: Public on Feb 20 2009

city: Pittsburgh

first: Kazuhisa

last: Konishi

state: PA

address: 1212 Kaufmann Building  3471 Fifth Ave

department: Pulmonry, Allergy, and Critical Care Medicine

country: USA

institute: University of Pittsburgh

summary:
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibrotic lung disease associated with significant morbidity and mortality.  We identified a combinatorial signature of 5 proteins that was sufficient to distinguish IPF patients from controls; of these proteins MMP7 and MMP1 exhibited significantly higher values in both peripheral blood concentrations and lung tissue gene expression,  suggesting their role as true biomarkers.
Keywords: disease versus control

overall_design:
Lung tissue samples for microarray analysis were obtained through the
University of Pittsburgh Health Sciences Tissue Bank. Twenty-three samples were obtained from surgical remnants of biopsies or lungs explanted from patients with IPF who underwent pulmonary transplant, eight patients with idiopathic pulmonary fibrosis whose pathological findings were indicative of the acute exacerbations, and 15 control normal lung tissues obtained from the disease free margins with normal histology of lung cancer resection specimens. The morphologic diagnosis of IPF was based on typical microscopic findings consistent with usual interstitial pneumonia.
Total RNA was used as a template for synthesis of cDNA as recommended by the manufacturer of the arrays (Agilent Technologies, Santa Clara, CA). The cDNA was used as a template to generate Cy3 labeled cRNA that was used for hybridization on Agilent Whole Human Genome 4 X 44K multi pack arrays (Agilent Technologies, Santa Clara, CA). After 17 hours hybridization, arrays were washed and scanned according to the manufacturer’s protocol.

first: Thomas

middle: J

last: Richards

first: Naftali

last: Kaminski


title: Gene expression in the Anopheles gambiae embryo

status: Public on Feb 26 2009

city: Berkeley

first: Yury

last: Goltsev

state: CA

address: 585 LSA, UC Berkeley

department: MCB

institute: UC Berkeley

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

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Refer to individual Series


title: PBMC response to B. pertussis filamentous hemagglutinin stimulation in vitro

status: Public on Oct 30 2008

city: Palo Alto

last: Dieterich

address: 3801 Miranda Avenue

department: Department of Microbiology & Immunology

institute: VA hospital

summary:
Filamentous hemagglutinin (FHA), Bordetella pertussis' key adhesin, is both present at the cell surface and released in the extracellular milieu. To comprehend the role free FHA plays in the pathogenic process, we analyzed the global transcriptional changes in human peripheral blood mononuclear cells (PBMC) after exposure to that purified virulence factor.  This analysis was undertaken with four different FHA preparations (FHA-1, FHA-2, FHA-3, and FHA-4), purified from four different B. pertussis strains. Cultures comprising 3x106 PBMC were stimulated for 0.5, 2, 4, and 6 hours with 5 ug/ml of each purified B. pertussis FHA. Control PBMC cultures were simultaneously treated with similar volumes of elution buffers (Mock-1 and Mock-2), and sampled at the same time points. The array experiment was composed of 27 samples.   Most of the transcripts known to be part of the "common host-transcriptional response" that mediates inflammation were among the 1,235 array elements (representing 683 known unique genes) showing a greater than 3-fold change in transcript abundance between FHA-treated and untreated cells. We also identified an FHA-specific signature not observed in cells stimulated with B. pertussis LPS or heat-killed B. pertussis. This response, mounted by 13 genes, largely (69%, 9/13 genes) interferon (IFN)-regulated genes. Further analysis revealed that 18.3% (125 out of 683) of the FHA-responsive genes were in fact regulated by IFN. These included several major players of the antiviral IFN type I response, as well as three key components of the ISGylation pathway. Induction of the ubiquitin-like protein ISG15 and its specific protease USP18 was confirmed at the mRNA level by relative real-time polymerase chain reaction (RT-PCR). Western-blot analysis demonstrated the presence of both free ISG15 and several ISGylated conjugates in FHA-stimulated PBMC cell lysate. Intracellular FACS analysis provided further evidence that monocytes and a natural-killer (NK)-enriched cell population are the primary producers of ISG15 after FHA stimulation.  Our results revealed new activities of free B. pertussis FHA: activation of the host IFN and ISGylation pathways. The consequences of such activation are yet to be resolved, but we hypothesize that FHA utilizes the ISGylation pathway or USP18 to regulate the IFN response, which in turn sensitizes the host to the infection and induces cell death.
Groups of assays that are related as part of a time series.
Infection: treatment with purified B. pertussis filamentous hemagglutinin (FHA) at 0.005 mg/mL
Time: Samples were collected after various treatment time (hours)
Keywords: time_series_design

overall_design: Computed

first: David

middle: A

last: Relman


title: Stress response in yeasts

status: Public on Sep 01 2008

city: Paris

first: Gaëlle

last: Lelandais

address: 2, place Jussieu

country: France

institute: INSERM

summary:
Transcriptome response of the yeasts C. glabrata and S. cerevisiae treated by an antifungal agent, benomyl
Keywords: time course; stress response

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: We performed microarray analyses of the transcriptome response of the yeasts Candida glabrata and Saccharomyces cerevisiae, treated by an antifungal agent, benomyl. The C. glabrata cells were submitted to 20 μg/mL of benomyl for 2, 4, 10, 20, 40 and 80 minutes. The labelled cDNA from treated cells were competitively hybridized on microarrays versus cDNA from mock treated cells.

first: Frédéric

last: Devaux


title: Alterations in gene expression profiles of immature human monocytes (U937) following 12/15-lipoxygenase expression.

status: Public on May 30 2008

city: Berlin

first: Pavlos

last: Chaitidis

address: Monbijoustr. 2

department: University Clinics Charite, Humboldt University

country: Germany

institute: Institute of Biochemistry

summary:
Lipoxygenases (LOX) form a heterogeneous family of lipid peroxidizing enzymes capable of converting polyunsaturated fatty acids to their hydroperoxy derivatives. They have been implicated in basic cellular processes such as proliferation and differentiation but are also involved in the pathogenesis of various diseases such as inflammatory disorders and atherosclerosis. The catalytic activity of LOXs increases the intracellular peroxide tone, which is an important parameter for expression regulation of redox-sensitive genes. Previously, we showed that induction of 12/15-expression by interleukin-4 profoundly alters the gene expression pattern of human peripheral monocytes, which led to a profound switch of the cellular phenotype. To explore, which of these changes might be a direct consequence of 12/15-LOX expression we stably transfected a permanent human monocytic cell line (U937) with a 12/15-LOX containing eukaryotic expression plasmid and an empty control vector (mock-control). After a multi-step selection procedure a viable clones (12/15-LOX transfectants and mock-transfectants) were isolated and further cultured. We found that 12/15-LOX expression did not significantly alter basic cellular functions and that the cells, which express the 12/15-LOX at similar levels as IL4-treated human monocytes, did not show major functional deficits when compared with the mock-transfectants. However, more detailed comparison of the gene expression profiles of 12/15-LOX transfected cells and that of corresponding mock-transfectants revealed subtle differences. Among the 22,300 genes present on the chip about one half was not expressed regardless whether 12/15-LOX was present in the cells or not. In 12/15-LOX expressing cells 11,000 genes (50 % of the genes present on the chip) and in the corresponding mock-transfectants 10,600 genes (47 % of the genes present on the chip) were expressed. Among the expressed genes only 900 (7 %) were upregulated more than 2-fold and 1,400 (12 %) were down regulated to a similar extent. Among the regulated gene products we detected several connective tissue matrix proteins (collagen isoforms, lamins, fibulins, fibronectins, aggrecans, claudins), extracellular proteinases (serpins, matrix metalloproteinases), tissue inhibitors of metalloproteinases, growth factors and their receptors, and adhesion molecules. In most cases, we did not see simultaneous up- or down-regulation of all family members but rather selective regulatory response of individual proteins (for instance 5-fold upregulation of collagen XV, alpha –1, but 20-fold downregulation of collagen VII, alpha-1 after 12/15-LOX transfection). These data suggest that induction of 12/15-LOX specifically modifies the gene expression pattern of U937 cells but did not lead to comprehensive alterations.
Keywords: other

overall_design:
Cell transfection
The eukaryotic expression vector pcDNA 3 (Invitrogen Life Technologies,
Leek, The Netherlands) bearing the complete coding region of the rabbit
reticulocyte type 15-LOX1 and a corresponding empty vector (mock) were
transfected into U937 cells using FuGENE 6, according to the manufacturer’s instructions.
Briefly, 2.5 x 10E5 cells/ml were plated on 35-mm plates and transfected with 2 µg of plasmid using 6 µl of FuGENE 6 reagent. After 72h exposure, the precipitate was removed and the cells were cultured for 4 weeks in selection medium supplemented with 0.5 mg/ml geneticin.
Incubation: 	at 37 °C with 5% CO2

first: Ralf

last: Kuban

first: Hartmut

last: Kuhn


title: Prediction and verification of mouse tRNAs identifies intron-containing families

status: Public on Feb 22 2008

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

summary:
Computer algorithms are often used to identify tRNA genes in newly sequenced genomes, but these predictions can be challenging.  Not only are there structural variations and extremely limited sequence conservation among genes, but vertebrate genomes tend to have highly reiterated short interspersed sequences (SINEs) that originally derived from tRNA genes or tRNA-like transcription units.  We have employed two programs, tRNAScan SE and ARAGORN, to predict the tRNA genes in the mouse nuclear genome, resulting in quite diverse but overlapping predicted gene sets.  From these, we removed known SINE repeats and sorted the genes into predicted families and single-copy genes.  In particular, four families of intron-containing tRNA genes were predicted, with introns in positions and structures analogous to the well characterized intron-containing tRNA genes in yeast.  In this work we focus on verifying the expression of the intron-containing tRNA gene familes, as well as the other 30 tRNA gene familes.
Keywords: tRNA, direct label

overall_design: Total RNa from 12 tissues was screened by microarray for predicted tRNAs.

first: D

last: Coughlin

first: T

first: C

last: Nihranz

middle: R

last: Hughes

last: Engelke


title: Mycobacterium tuberculosis and macrophage response

status: Public on Mar 27 2008

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ


title: A Survey of Genetic Human Cortical Gene Expression

status: Public on Nov 04 2007

city: Miami

first: Amanda

last: Myers

state: FL

address: 1600 NW 10th Ave

department: Psychiatry and Behavioral Sciences

institute: Miller School of Medicine, University of Miami

summary:
It is widely assumed that genetic differences in gene expression will underpin much of the differences between individuals and many of the quantitative traits of interest to geneticists.  Despite this, there has been little work on genetic variability in human gene expression and almost none in the human brain.  This is because the tools for assessing this genetic variability were not available.  With whole genome SNP genotyping arrays and whole transcriptome expression arrays, these experiments have now become feasible. We have carried out whole genome genotyping and expression analysis on a series of 193 neuropathologically normal human brain samples using the Affymetrix GeneChip Human Mapping 500K Array Set and Illumina HumanRefseq-8 Expression BeadChip platforms.  Here we present data showing that 58% of the transcriptome is cortically expressed in at least 5% of our samples, and of these cortically expressed transcripts 21% have expression profiles that correlate with their genotype. These genetic expression effects should be useful in determining the underlying biology of associations with common diseases of the human brain and in guiding the analysis of the genomic regions involved in the control of normal gene expression.
Keywords: neuropathologically normal cortex

overall_design: RNA ws isolated from human cortical samples by standard protocols. RNA expression was assessed using the Illumina HumanRefseq-8 Expression BeadChip system.  Transcripts that were detected in less than 5% of the series were excluded from our study. All expression profiles were extracted and rank invariant normalized (Workman et al 2002, Shadt et al 2001, Tseng et al 2001) using the BeadStudio software available from Illumina (http://www.illumina.com/pages.ilmn?ID=170).

first: Jesse

last: Gibbs

first: Jennifer

last: Webster

first: Kristen

last: Rohrer

first: Alice

last: Zhao

first: Lauren

last: Marlowe

first: Mona

last: Kaleem

first: Doris

last: Leung

first: Leslie

last: Bryden

first: Priti

last: Nath

first: Victoria

middle: L

last: Zismann

first: Keta

last: Joshipura

first: Matthew

last: Huentelman

first: Diane

last: Hu-Lince

first: Keith

middle: D

last: Coon

middle: W

last: Craig

first: John

middle: V

last: Pearson

first: Peter

last: Holmans

first: Christopher

middle: B

last: Heward

first: Eric

middle: M

last: Reiman

first: Dietrich

last: Stephan

last: Hardy


title: Gene-environment interaction in yeast gene expression

status: Public on Apr 15 2008

city: Princeton

first: Erin

middle: N

last: Smith

address: 110 Carl Icahn Labs

department: Ecology and Evolutionary Biology

institute: Princeton University

summary:
This study is a quantitative trait linkage mapping study targeted at gene-environment interaction. A family of yeast derived from BY4716 and RM11-1a was grown in two carbon sources (glucose and ethanol) and expression profiled. The analysis revealed how the influence of genetic factors changes in different conditions.

Abstract:
The effects of genetic variants on phenotypic traits often depend on environmental and physiological conditions, but
such gene–environment interactions are poorly understood. Recently developed approaches that treat transcript abundances of thousands of genes as quantitative traits offer the opportunity to broadly characterize the architecture
of gene–environment interactions. We examined the genetic and molecular basis of variation in gene expression between two yeast strains (BY and RM) grown in two different conditions (glucose and ethanol carbon sources). We
observed that most transcripts vary by strain and condition, with 2,996, 3,448, and 2,037 transcripts showing significant strain, condition, and strain–condition interaction effects, respectively. We expression profiled over 100
segregants derived from a cross between RM and BY in both growth conditions, and identified 1,555 linkages for 1,382 transcripts that show significant gene–environment interaction. At the locus level, local linkages, which usually
correspond to polymorphisms in cis-regulatory elements, tend to be more stable across conditions, such that they are more likely to show the same effect or the same direction of effect across conditions. Distant linkages, which usually
correspond to polymorphisms influencing trans-acting factors, are more condition-dependent, and often show effects in different directions in the two conditions. We characterized a locus that influences expression of many growth-
related transcripts, and showed that the majority of the variation is explained by polymorphism in the gene IRA2. The RM allele of IRA2 appears to inhibit Ras/PKA signaling more strongly than the BY allele, and has undergone a change in
selective pressure. Our results provide a broad overview of the genetic architecture of gene–environment interactions, as well as a detailed molecular example, and lead to key insights into how the effects of different classes of regulatory
variants are modulated by the environment. These observations will guide the design of studies aimed at understanding the genetic basis of complex traits.
Keywords: QTL

overall_design:
This data set includes 24 parental arrays (6 of each parent in each condition, 218 segregant arrays (109 in both conditions), and 4 allele replacement arrays (IRA2 replacements in both backgrounds in both conditions).

All arrays are from an unique biological sample, and many are randomized for dye (no dye-swaps on the same RNA sample). For the 24 parental arrays, there are three of each strain*condition*dye combination. The segregant arrays were randomized for dye. The replacement arrays are all of the Cy5 = experimental, Cy3 = reference type. All arrays are hybridized to a common reference consisting of an equal portions of RNA samples. from BY and RM grown in glucose and ethanol.

Analysis was performed using default settings in Agilent Feature Extractor software versions 8.0-9.5. Spots were excluded if their intensity was below 350 or if they were flagged as non-uniformity outliers. Transcripts were considered good if they were present in all parental arrays (for the parental analysis) or 80% of all arrays in each condition for the segregant analysis.

first: Leonid

last: Kruglyak


title: Regional gene expression in the Xenopus gastrula

status: Public on Nov 01 2007

city: Bethesda

first: Hui

last: Zhao

state: MD

address: 9000 Rockville Pike

department: NICHD

institute: NIH

summary:
Studies on the early embryonic development of Xenopus laevis contributed much to the understanding of vertebrate patterning. Gastrula stages are of particular interest because establishment of the axis and germ layer formation take place during these stages. While many genes belonging to several signaling pathways including FGF, Wnt and TGF-beta, have been implicated in patterning the gastrula embryo, the hierarchical interactions between these factors are incompletely known. To study this question, we took advantage of microarray technology to create a regional gene expression profile for the Xenopus gastrula.
Stage 10 Xenopus embryos were dissected into four portions. The dorsal marginal zone including the blastopore and some ectoderm and dorsal yolk plug, composed mostly of endomesoderm; the ventral marginal zone, also containing a portion of the yolk plug; the animal cap, dissected just above the floor of the blastocoel; and the vegetal region, composed of the central part of the yolk plug. To avoid possible cross contamination that might blur the microrarray data, thin junctional regions between the explants were removed. The dissected explants were homogenized in Stat 60 (TEL TEST), RNA was precipitated by isopropanol, treated with DNase I, and purified using the RNeasy kit (Qiagen). Biotinylated probe was prepared from 100 ng total RNA using the OVATION RNA amplification system (Nugen Technologies, Inc). The probes were hybridized to Affymetrix Xenopus Chips containing features that represent about 15,000 genes according to the manufacture’s instructions. Hybridized arrays were further processed by the GeneChip Fluidics system (Affymetrix), and signals were detected by the GeneChip Scanner (Affymetrix). Gene expression profiles were analyzed by the GCOS software (Affymetrix).
The analysis showed that 100 transcripts were enriched in the dorsal explant (dorsal vs. ventral, signal log2 ratio>1.5), including the known dorsal markers Chordin, gsc, Admp; 90 transcripts were enriched in the ventral explant (ventral vs. dorsal, signal log2 ratio>1.5) including Sizzled, bambi, PV.1; 449 transcripts were enriched in the vegetal explant (vegetal vs. dorsal, vegetal vs. ventral, vegetal vs. animal cap, all signal log2 ratio>1.5), including Mixer, Sox17; 70 transcripts were enriched in the animal cap (animal cap vs. vegetal, signal log2 ratio>1.5; animal cap vs. dorsal, signal log2 ratio>1; animal cap vs. ventral, signal log2 ratio>1) including Epidermal type I cytokeratin and forkhead-2.  RT-PCR was used to check the enrichment of some of the unknown genes; the enrichment of 8 of 9 ventral genes, and 9 of 12 dorsal genes was confirmed in these experiments.
Keywords: Xenopus, gastrula, explant, gene expression, embryonic, gene regulation

overall_design: Ceate a regional gene expression profile in Xenopus gastrula, and predict gene expression pattern by comparing gene expression in different explant.

first: Kosuke

last: Tanegashima

first: Igor

last: Dawid


title: Expression of microRNAs and Protein-coding Genes Associated with Perineural Invasion in Prostate Cancer

status: Public on Jul 01 2008

first: Robert

middle: Scott

last: Hudson

address: National Cancer Institute Room Blgd.37/3044

department: NCI

type: Expression profiling by high throughput sequencing

summary:
BACKGROUND. Perineural invasion (PNI) is the dominant pathway for local invasion in prostate cancer. To date, only few studies have investigated the molecular differences between prostate tumors with PNI and those without it.
METHODS. To evaluate the involvement of both microRNAs and protein-coding genes in PNI, we determined their genome-wide expression with a custom microRNA microarray and Affymetrix GeneChips in 50 prostate adenocarcinomas with PNI and 7 without it. In-situ hybridization and immunohistochemistry was used to validate candidate genes.
RESULTS. Unsupervised classification of the 57 adenocarcinomas revealed two clusters of tumors with distinct global microRNA expression. One cluster contained all non-PNI tumors and a subgroup of PNI tumors. Significance analysis of microarray data yielded a list of microRNAs associated with PNI. At a false discovery rate (FDR) < 10%, 19 microRNAs were higher expressed in PNI tumors than in non-PNI tumors. The most differently expressed microRNA was miR-224. In-situ hybridization showed that this microRNA is expressed by perineural cancer cells. The analysis of protein-coding genes identified 34 transcripts that were differently expressed by PNI status (FDR <10%). These transcripts were down-regulated in PNI tumors. Many of those encoded metallothioneins and proteins with mitochondrial localization and involvement in cell metabolism. Consistent with the microarray data, perineural cancer cells tended to have lower metallothionein expression by immunohistochemistry than nonperineural cancer cells.
CONCLUSIONS. Although preliminary, our findings suggest that alterations in microRNA expression, mitochondrial function, and cell metabolism occur at the transition from a non-invasive prostate tumor to a tumor with PNI.
Keywords: Disease State analysis

platform_organism:
Homo sapiens
Mus musculus

overall_design: Frozen tumor specimens were obtained from the NCI Cooperative Prostate Cancer Tissue Resource (CPCTR). RNA from these patient, 7 of which had no Perineural invasion, were hybridized to both Affymetrix and miRNA microarrays to explore the underlying molecular events associated with perineural invasion.

first: Stefan

last: Ambs

middle: S

first: Robyn

last: Prueitt

first: Ming

last: Yi


title: Gene expression in brain following stroke

status: Public on Oct 29 2007

city: Manchester

first: Nick

last: Mitsios

address: Chester Street

country: United Kingdom

institute: Manchester Metropolitan University

summary:
We have used microarrays to investigate the changes in gene expression at various times after stroke. Our findings reported that gene expression screening can detect known and unknown transcriptional features of stroke.
Keywords: time course, disease state analysis

overall_design: Brain samples were obtained from 9 patients who died from stroke, with the approval of the local Ethics Committee. The patients were aged between 51 and 86 years and had survived between 2-37 days following stroke. Tissue samples were taken from infarct and peri-infarcted zones while controls were obtained from the contralateral hemisphere. We established mRNA expression profiles of the damaged brain tissues between 2 to 6 days, 9 to 20 days, and 26 to 37 days after stroke. RNA from three stroke patients was pooled for each patient survival group.

first: Jurek

last: Krupinski

last: Gaffney

first: Pat

last: Kumar

first: Shant

first: Mark

last: Slevin


title: Expression data from Lung cancer

status: Public on Aug 30 2007

city: Taipei

first: Li-Jen

last: Su

address: No. 201, Sec. 2, Shih-Pai Road

department: Department of Surgery

country: Taiwan

institute: Taipei Veterans General Hospital

summary:
Detection, treatment, and prediction of outcome for lung cancer patients increasingly depend on a molecular understanding of tumor development and sensitivity of lung cancer to therapeutic drugs. The application of genomic technologies, such as microarray, is widely used to monitor global gene expression and has built up invaluable information and knowledge, which is essential to the discovery of new insights into the mechanisms common to cancer cells, resulting in the identification of unique, identifiable signatures and specific characteristics. It is likely that application of microarray may revolutionize many aspects of lung cancer being diagnosed, classified, and treated in the near future. We used microarrays to detail the global gene expression patterns of lung cancer.
Keywords: Disease state analysis

overall_design: Adjacent normal-tumor matched lung cancer samples were selected at early and late stages for RNA extraction and hybridization on Affymetrix microarrays. A total of 66 samples were used for microarray analysis, including pairwise samples from 27 patients, who underwent surgery for lung cancer at the Taipei Veterans General Hospital, two tissue mixtures from the Taichung Veterans General Hospital (one was adjacent normal lung mixtures and the other was lung adenocarcinoma mixtures), two commercial human normal lung tissues (Clontech (Catalog No. 636524) and Stratagene (Catalog No. 735020)), one immortalized, nontumorigenic human bronchial epithelial cell line (NL-20 (ATCC® No. CRL-2503)), and 7 lung cancer cell lines (A-549 (ATCC® No. CCL-185), NCI-H1299 (ATCC® No. CRL-5803), NCI-H661 (ATCC® No. HTB-183), CL1-0, CL1-1, CL1-5 and CL1-5-F4.

first: Chi-Ying

middle: F

last: Huang

first: Yu-Chung

last: Wu


title: Patterns of gene expression following contact of sympathetic neurons with their myocyte targets

status: Public on Jul 31 2007

city: Waltham

first: Susan

last: Birren

state: MA

address: 415 South st

department: Biology

institute: Brandeis University

summary:
We identified 112 known genes and 150 expressed sequence tags (ESTs) showing more than a 1.3 fold change in target-exposed neurons compared to neurons grown in the absence of target.  Expression of 36 genes and 49 ESTs was upregulated, while expression of 76 genes and 101 ESTs was downregulated by the presence of target during the culture period. Overall, these changes represented approximately 1.6% of the probe set.
Keywords: Patterns of gene expression by neuron-target interaction

overall_design:
We investigated the molecular basis of the target-regulated growth inhibition program using DNA microarrays to analyze patterns of gene expression following contact of sympathetic neurons with their myocyte targets. Total RNA was isolated from sympathetic neurons cultured alone and from neurons isolated from myocyte co-cultures.  The two neuron populations showed minimal levels of atrial natriutic peptide (ANF) mRNA, a myocyte marker, compared to myocyte-containing cultures, indicating a low level of myocyte contamination for neurons purified from co-cultures.
Isolated total RNA was reverse transcribed, labeled with biotin by in vitro transcription and hybridized to an Affymetrix Rat Expression Set 230A microarray with 15,900 probe sets. The hybridized microarray was washed, stained, scanned and quantified using DNA-Chip Analyzer (dChip) 1.3 (Li and Wong, 2001).

first: Jung-Il

last: Moon


title: miRNA expression in head and neck squamous cell carcinoma (HNSCC)

status: Public on Sep 30 2008

city: Providence

first: Michele

last: Avissar

state: RI

address: 70 Ship Street

department: Pathology

institute: Brown University

summary:
The involvement of microRNAs (miRNAs) in cancer and their potential as biomarkers of diagnosis, prognosis and response to therapy is becoming increasingly appreciated. The etiology of head and neck squamous cell carcinoma (HNSCC) is predominantly associated with the synergistic effects of tobacco and alcohol use, as well as Human Papilloma Virus (HPV) infection, which embodies a distinct clinical and biological phenotype. We sought to examine whether the profile of miRNAs in HNSCC varies based on HPV status, and to identify specific miRNAs altered in head and neck carcinogenesis. Total RNA was isolated from 16 HNSCC fresh frozen primary tumors, 5 fresh frozen non-diseased head and neck epithelial tissues, and 2 HNSCC cell lines.  The miRNA profile of 662 individual miRNAs in these tissues was examined by microarray. 18 miRNAs are significantly altered in their expression between normal tissues and HNSCC tumors and 5 miRNAs are identified as significantly differentially expressed between HPV-positive (HPV+) and HPV-negative (HPV-) tumors. A striking difference in expression pattern of miRNA was also observed between primary tissues and cell lines.  These data suggest that the pattern of miRNA expression may be reflective of disease etiology, and may be useful in the realm of diagnostic biomarkers defining broadly responsive prevention and treatment strategies for HNSCC.  These data also suggest that cultured tumor cell lines may be inappropriate for novel miRNA biomarker identification.
Keywords: miRNA; Disease-state analysis

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Expression of 662 individual miRNA was assessed in16 HNSCC fresh frozen primary tumors, 5 fresh frozen non-diseased head and neck epithelial tissues, and 2 HNSCC cell lines were arrayed

first: Brock

middle: C

last: Christensen

first: Karl

middle: T

last: Kelsey

first: Carmen

last: Marsit


title: Gene expression analysis during differentiation of EPC to OEC

status: Public on Sep 24 2008

city: Seoul

first: Young-Guen

last: Kwon

address: 262 Seongsanno, Seodaemun-Gu

department: Dppartment of Biochemistry

country: South Korea

institute: Yonsei University

summary: Gene expression profiles during the differentiation of EPCs into OECs were analyzed.

overall_design: RNA was isolated from Human cord blood derived- EPC and differentiated OEC from EPC. HG-U133A 2.0 microarray (54675 human genes; Affymetrix Santa Clara, CA, USA) was performed.

first: Yong-Sun

last: Maeng


title: Comprehensive analysis of PPARα-dependent regulation of hepatic lipid metabolism by expression profiling - 4

status: Public on Jul 24 2007

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
PPARα is a ligand-activated transcription factor involved in the regulation of nutrient metabolism and inflammation. Although much is already known about the function of PPARα in hepatic lipid metabolism, many PPARα-dependent pathways and genes have yet to be discovered.  In order to obtain an overview of PPARα-regulated genes relevant to lipid metabolism, and to probe for novel candidate PPARα target genes, livers from several animal studies in which PPARα was activated and/or disabled were analyzed by Affymetrix GeneChips. Numerous novel PPARα-regulated genes relevant to lipid metabolism were identified. Out of this set of genes, eight genes were singled out for study of PPARα-dependent regulation in mouse liver and in mouse, rat, and human primary hepatocytes, including thioredoxin interacting protein (Txnip), electron-transferring-flavoprotein β polypeptide (Etfb), electron-transferring-flavoprotein dehydrogenase (Etfdh), phosphatidylcholine transfer protein (Pctp), endothelial lipase (EL, Lipg), adipose triglyceride lipase (Pnpla2), hormone-sensitive lipase (Lipe), and monoglyceride lipase (Mgll). Using an in silico screening approach, one or more PPAR response elements (PPREs) were identified in each of these genes.  Since Pnpla2, Lipe, and Mgll contribute to hepatic triglyceride hydrolysis, gene regulation was studied under conditions of elevated hepatic lipids. In wild-type mice fed a high fat diet, the decrease in hepatic lipids following treatment with the PPARα agonist Wy14643 was paralleled by significant up-regulation of Pnpla2, Lipe, and Mgll, suggesting that induction of triglyceride hydrolysis may contribute to the anti-steatotic role of PPARα. Our study illustrates the power of transcriptional profiling to uncover novel PPARα-regulated genes and pathways in liver.
Keywords: identification of target genes

overall_design:
3-5 months old male pure bred wild-type (129S1/SvImJ) and PPARα-null (129S4/SvJae) mice were used.
Wild-type and PPARα-null mice were treated with the synthetic PPARα ligand Wy14643 (0.1% w/w) mixed in the food, or normal food (control) for 5 days (n=4 per group). Liver total RNA from biological replicates was hybridized onto Affymetrix mouse genome 430 2.0 GeneChip arrays.
Five microgram total RNA was labelled according to the ENZO-protocol, fragmented and hybridized according to Affymetrix's protocols.

first: Maryam

last: Rakhshandehroo

first: Linda

last: Sanderson

first: Merja

last: Matilainen

first: Rinke

last: Stienstra

first: Carsten

last: Carlberg

first: Philip

last: de Groot

first: Michael

last: Muller

first: Sander

last: Kersten


title: Using FlyAtlas to identify better Drosophila models of human disease

status: Public on Jun 21 2007

city: Glasgow

first: Jing

last: Wang or Venkat Chintapalli

state: Scotland

address: Dumbarton Road

department: Molecular Genetics

institute: University of Glasgow

summary: A new online resource (flyatlas.org) provides the most comprehensive view yet of expression in multiple tissues of Drosophila. Meta-analysis of the data reveals that a significant fraction ofthe genome is expressed with great tissue specificity in the adult, demonstrating the need for the functional genomic community to embrace a wider range of functional phenotypes. Well-known developmental genes are often re-used in surprising tissues in the adult, suggesting new functions. The homologues of many human genetic disease loci show selective expression in  Drosophila tissues with function analogous to the affected tissues in the cognate human disease, providing a useful filter for potential candidate genes.

overall_design: FlyAtlas is composed of data so far covering 31 distinct adult and larval tissues with 4 replicates on run using Affymetrix Dros Genome 2 chips, and compared with a matched whole-fly sample. The resource is continuosly extended with the funding secured until 2010.

first: Venkateswara

last: Chintapalli

last: Wang

first: Julian

last: Dow


title: Recovery growth

status: Public on Jan 31 2007

city: Rennes

first: Pierre-Yves

last: Rescan

address: Campus de Beaulieu

institute: INRA

summary:
We used cDNA microarrays to describe the changes in gene expression in muscle during recovery growth induced by a fasting-refeeding sequence.
Keywords: muscle, fasting-refeeding, time-course

overall_design: Muscle of trout fasted for one month (cplx_J0-10, cplx_ J0-2, cplx_J0-3, cplx_J0-4, cplx_J0-5, cplx_J0-6, cplx_J0-7,cplx_ J0-8).  Muscle of  trout fasted for one month and then refed for 4 days (cplx_J4-1, cplx_J4-2, cplx_J4-3, cplx_J4-4, cplx_J4-5,cplx_ J4-6, cplx_J4-7, cplx_J4-8, cplx_J4-9), 7 days (cplx_J7-10, cplx_J7-2, cplx_J7-3, cplx_J7-4, cplx_ J7-5, cplx_ J7-6, cplx_ J7-7, cplx_ J7-8, cplx_J7-9), 11 days (cplx_J11-10, cplx_ J11-2, cplx_J11-3, cplx_J11-4, cplx_ J11-5, cplx_J11-6, cplx_J11-7, cplx_J11-9) and 36 days (cplx_J36-10, cplx_J36-2, cplx_ J36-3, cplx_J36-4, cplx_J36-5, cplx_J36-6, cplx_J36-7, cplx_J36-8, cplx_J36-9).


title: Transcriptional profiling of rhesus monkey nuclear transfer embryonic stem cells

status: Public on Aug 29 2007

city: Beaverton

first: James

middle: Anthony

last: Byrne

state: OR

address: 505 NW 185th Ave

department: Reproductive Sciences

institute: ONPRC

summary:
Derivation of embryonic stem cells (ESC) genetically identical to a patient by somatic cell nuclear transfer (SCNT) holds the potential to cure or alleviate the symptoms of many degenerative diseases while circumventing any immunorejection issues.  However, no primate nuclear transfer embryonic stem (ntES) cell lines have been derived to date.  Here, we used a modified SCNT technique to produce rhesus macaque SCNT blastocysts at a relatively high efficiency from adult donor cells and we successfully derived two primate ntES cell lines from 304 oocytes (an overall efficiency of 0.7%).  Nuclear and mitochondrial DNA analysis confirmed the ntES cell lines were derived from rhesus monkey SCNT blastocysts and both rhesus monkey ntES cell lines exhibited a normal ESC morphology, expressed key stemness markers, were transcriptionally indistinguishable from control ESC lines and differentiated into multiple cell types.  This is, to our knowledge, the first confirmed derivation of primate ntES cell lines.
Keywords: rhesus monkey somatic cell nuclear transfer embryonic stem cells

overall_design: We compared the transcriptomes of rhesus monkey embryonic stem cell lines derived from IVF-produced embryos (ORMES-10 and ORMES-22) with rhesus monkey nuclear transfer embryonic stem cells derived from somatic cell nuclear transfer produced embryos (CRES-1 and CRES-2).  We also analyzed the donor adult somatic skin fibroblast cell line used to produce the cloned embryos.  Three biological replicates of each cell line (A, B and C) was analyzed.

first: Darlene

last: Perdersen

first: Lisa

last: Clepper

first: Don

last: Wolf

first: Shoukhrat

last: Mitalipov


title: Molecular Features of Hormone-Refractory Prostate Cancer Cells by Genome-wide Gene-expression Profiles

status: Public on Jun 01 2007

city: Tokyo

first: Hidewaki

last: Nakaagwa

state: Tokyo

address: 4-6-1 Shirokanedai, Minato-ku,

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

summary:
To characterize the molecular features of clinical (Hormone-Refractory Prostate Cancers) HRPCs, we generated the precise gene-expression profiles of 25 clinical HRPCs and 10 hormone-sensitive prostate cancers (HSPCs) by genome-wide cDNA microarrays combining with laser microbeam microdisection.
Keywords: disease status analysis

overall_design:
25 clinical HRPC tissues were procured from 18 HRPC patients through prostate biopsy, TUR-P, bone biopsy, or warm autopsy. We microdissected cancer cells from these frozen slices by means of LMM (laser microbeam microdissection) system (EZ cut system with a pulsed ultraviolet narrow beam-focus laser, SL Microtest GmbH, Germany). Simultaneously, 10 hormone-sensitive or -naïve prostate cancers (HSPCs) were also microdissected from 10 untreated operable cases undergoing radical prostatectomy. Normal prostatic epithelial cells were also microdissected from one benign prostatic hyperplasia (BPH) patient and four bladder cancer patients, where we confirmed no apparent prostate cancers or PINs histopathologically, and we used the RNA mixtures of these microdissected normal prostate epithelial cells as a reference of cDNA microarray analysis.

Extraction protocol
100,00-200,000 tumor cells or normal cells were isolated selectively using the EZ cut system with a pulsed ultraviolet narrow beam-focus laser (SL Microtest GmbH, Germany) in accordance with the manufacturer’s protocols. Total RNAs were isolated from captured cells with QIAGNE RNAeasy Kit (QIAGEN). After DNAse I treatment, total RNAs were subjected to two rounds of T7-based amplification using MEGAscript High Yield Transcription Kit (Ambion), which yielded 50-100 ug of amplified RNA (aRNA) from each sample.

Label protocol
2.5 ug aliquots of aRNA from tumor cells or normal cells were annealed with random primer for 10 min at 70oC. They were labeled in a 50ul volume by reverse transcription reaction for 2 hours at 37oC using Superscript II reverse transcriptase (Invitrogen) with 1mM Cy5-dCTP for tumor cells or Cy3-dCTP for normal cells (Amersham) and 25mM each dATP, dGTP, and dTTP. The labeling reaction was stopped by adding 6ul 2.5 N NaOH and incubation for 30 min at 65oC and neutralized by 20ul 1M Tris-HCl (pH7.4) and 7ul 2.5N HCl. The labeled cDNAs were purified by QIAquick PCR Purification Kit (QIAGEN).

Hybridization protocol
Labeled cDNAs were mixed with microarray hybridization solution version 2 (Amersham) and formamide (Sigma) to a final concentration of 50%. After hybridization for 14-16 hours at 42 oC in Automated Slide Processor, the slides were washed in 2xSSC and 1% SDS for 10min at 55 oC, washed in 0.2xSSC and 0.1% SDS for 10min at 55 oC, and washed in 0.1xSSC for 1 min at room temperature in Automated Slide Processor.

Scan protocol
Microarray slides were scanned using  the Array Scanner Generation III (Amersham) after hybridization.

Data processing
Images were gridded and the fluorescent intensity of each spot (Cy5/Cy3) was evaluated photometrically by the ArrayVision computer program (Imaging Research, Inc., St. Catharines, Ontario, Canada) . The fluorescent intensities of Cy5 (tumor) and Cy3 (control) for each target spot were adjusted so that the mean Cy3/Cy5 ratio of the 52 housekeeping genes was equal to one.  Because data derived from low signal intensities are less reliable, we determined a cut-off value on each slide and excluded genes from further analysis when both Cy3 and Cy5 dyes yielded signal intensities lower than the cut-off value. For other genes, we calculated the Cy5/Cy3 ratio using the raw data of each sample.

last: Nakagawa

first: Kenji

last: Tamura

first: Yusuke

last: Nakamura


title: Profiling sex-biased and developmental gene expression in Daphnia pulex

status: Public on Oct 06 2006

city: Bloomington

first: John

middle: Kenneth

last: Colbourne

state: IN

institute: Indiana University

summary:
We use a custom microarray for the crustacean Daphnia pulex to investigate gene expression in males, juvenile females and pregnant females.
Keywords: sex-biased, developmental

overall_design: Eight biological replicates of 8 day old healthy male Daphnia pulex are compared to four biological replicates of 8 day old healthy (pregnant) females, or to four biological replicates of healthy 6 day old (juvenile) females.  Each comparison involved two dye swaps: two males (green) vs. two pregnant females (red), two males (red) vs. two pregnant females (green) and so on.

first: Brian

last: Eads

middle: K

first: Elizabeth

last: Bohuski

first: Justen

last: Andrews


title: Definition of clinically distinct molecular subtypes in estrogen receptor positive breast carcinomas using genomic grade

status: Public on Mar 01 2007

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

summary:
Purpose: A number of microarray studies have reported distinct molecular profiles of breast cancers (BC): basal-like, ErbB2-like and two to three luminal-like subtypes. These were associated with different clinical outcomes. However, although the basal and the ErbB2 subtypes are repeatedly recognized, identification of estrogen receptor (ER)-positive subtypes has been inconsistent. Refinement of their molecular definition is therefore needed.

Materials and methods: We have previously reported a gene-expression grade index (GGI) which defines histological grade based on gene expression profiles. Using this algorithm, we assigned ER-positive BC to either high or low genomic grade subgroups and compared these to previously reported ER-positive molecular classifications. As further validation, we classified 666 ER-positive samples into subtypes and assessed their clinical outcome.

Results: Two ER-positive molecular subgroups (high and low genomic grade) could be defined using the GGI. Despite tracking a single biological pathway, these were highly comparable to the previously described luminal A and B classification and significantly correlated to the risk groups produced using the 21-gene recurrence score. The two subtypes were associated with statistically distinct clinical outcome in both systemically untreated and tamoxifen-treated populations.

Conclusions:  The use of genomic grade can identify two clinically distinct ER-positive molecular subtypes in a simple and highly reproducible manner across multiple datasets. This study emphasizes the important role of proliferation-related genes in predicting prognosis in ER-positive BC.
Keywords: disease state analysis

overall_design:
dataset of microarray experiments from primary breast tumors used to assess the reationship between GGI, molecular subtypes, and tamoxifen resistance.

No replicate, no reference sample.

first: Sherene

last: Loi

first: Christine

last: Desmedt

first: Françoise

last: Lallemand

first: Andrew

last: Tutt

first: Cheryl

last: Gillet

first: Paul

last: Ellis

first: Adrian

last: Harris

first: Jonas

last: Bergh

middle: A

last: Foekens

first: Jan

middle: G

last: Klijn

first: Denis

last: Larsimont

first: Marc

last: Buyse

first: Gianluca

last: Bontempi

first: Mauro

last: Delorenzi

first: Martine

middle: J

last: Piccart

first: Christos

last: Sotiriou


title: The global transcriptional profile of Mycobacterium tuberculosis during human macrophages infection

status: Public on Dec 18 2007

first: Virginie

middle: Marie

last: Aris

summary:
During lung infection Mycobacterium tuberculosis (Mtb) resides in macrophages and subverts the bactericidal mechanisms of these professional phagocytes.
In this work we have analyzed by DNA microarray technique the global transcription profile of Mtb infecting primary human macrophages in order to identify putative bacterial pathogenic factors that can be relevant for the intracellular survival of Mtb.
Keywords: time course

overall_design: We compared the global gene expression of the H37Rv strain of Mtb after 4 hours and 24 hours of infection of human macrophage-like THP-1 cells with the gene expression profile of the strain growing exponentially in broth cultures.

first: Patricia

last: Fontan

first: Saleena

last: Ghanny

last: Soteropoulos

first: Issar

last: Smith


title: Gene expression profiling in a congenic strain identifies candidate genes for nutrient intake QTL on mouse chromosome 17

status: Public on Dec 11 2007

city: Baton Rouge

first: Brenda

last: Richards

state: LA

address: 6400 Perkins Rd.

department: Basic Science

institute: Pennington Biomedical Research Center

summary:
The goal of this experiment was to identify genes contributing to fat, carbohydrate, and total calorie intake in mice by comparing gene expression in liver and hypothalamus of an interval-specific congenic strain, B6.CAST-17, with that of the control strain.  This congenic strain has previously confirmed genetic loci on Chr 17 linked to increased carbohydrate (Mnic1) and kilocalorie (Kcal2) intake.
Keywords: Comparative gene expression analysis

overall_design: RNA obtained from six male B6.CAST-17 homozygous congenic mice and six male wild type B6 mice was pooled.  Gene expression in hypothalamus and liver was compared between the strains under two diet conditions:  1) chow (LabDiet #5001) and 2) 78% carbohydrate/22% protein vs. 78% fat/22% protein, 4 h before lights out on day 2.  Mice were selected based on phenotypic variation; specifically, 20-25 mice of each strain were tested in a self-selection diet protocol for 10 days.  Mice that displayed the most divergent phenotypic values for nutrient intake (kcal per body weight) were chosen for study, returned to chow diet for 6 wks, and then returned to the 2-choice diet for one day.

first: Karunakaran

last: Kumar

last: Smith-Richards


title: HEK and HeLa cells:  transfection of siRNA directed against GFP versus mock transfection

status: Public on Aug 09 2007

city: Heidelberg

first: Cordula

last: Tschuch

address: Neuenheimer Feld 580

institute: DKFZ

summary:
We tested the most widely used control siRNA directed against GFP for off-target effects and found by genome-wide expression profiling  that it deregulates in addition to GFP a set of endogenous target genes. The detected modulated mRNA had target sequences homologous to the siRNA as small as 9 bp in size. However, we found no restriction of sequence homology to 3'UTR of target genes.
Keywords: RNAi knock down

overall_design: Two-condition experiment, siGFP transfected versus mock transfection, one replicate per array, one colour-switch per array


title: Gene Signature for Aggression of Melanoma Metastases - Melanoma Metastasis

status: Public on Oct 02 2007

city: cambridge

first: steve

last: shen

address: 77 mass ave

institute: MIT

summary:
Metastasis is the deadliest phase of cancer progression. Experimental models using immunodeficient mice have been used to gain insights into the mechanisms of metastasis. We report here the identification of a “metastasis aggressiveness gene expression signature” derived using human melanoma cells selected based on their metastatic potentials in a xenotransplant metastasis model. Comparison with expression data from human melanoma patients shows that this metastasis gene signature correlates with the aggressiveness of melanoma metastases in human patients. Many genes encoding secreted and membrane proteins are included in the signature, suggesting the importance of tumor-microenvironment interactions during metastasis.
Keywords: disease state

overall_design: test signature genereated from experiments of parental cell line vs xenograft model

first: Lei

last: Xu

first: Steven

last: Shen

first: Richard

last: Hynes


title: Expression data from embryonic rat kidney timepoints and a budded WD-MM recombination tissue

status: Public on Nov 30 2007

city: La Jolla

first: Sanjay

last: Nigam

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

summary:
Here we compared the expression of an engineered kidney tissue, created by recombining an in vitro budded Wolffian duct with fresh E13 metanephric mesenchyme, with that of three in vivo rat embryonic kidney timepoints (E13, E18, and week 4)
Keywords: time course

overall_design: The global gene expression of recombined tissue (non-branched in vitro-formed UBs and MM) was analyzed and compared to the gene expression of early, late, and post developmental kidneys in order to determine whether normal developmental pathways were being followed. Genes with at least a 3-fold difference in expression between any of the 4 conditions (E13, E18, Wk4, recombined tissue) were analyzed and grouped into one of ten expression patterns. The expression of each group of genes was analyzed in the recombined tissue to compare the recombined tissue gene expression levels to the three in vivo time points.


title: Methanococcus maripaludis response to hydrogen limitation

status: Public on Apr 01 2007

city: Seattle

first: John

last: Leigh

state: WA

department: Microbiology

institute: University of Washington

summary:
Methanococcus maripaludis is a methanogenic Archaea that conserves energy from molecular hydrogen to reduce carbon dioxide to methane. Chemostat grown cultures limited for hydrogen, phosphate, or leucine were compared to determine the regulatory response to hydrogen limitation. This was done by comparing hydrogen limited cultures to both leucine limited and phosphate limited cultures. Slow and rapid growing samples limited for either hydrogen or phosphate were compared to determine the regulatory effects of growth rate.
Keywords: archaea, hydrogen, leucine, phosphate, nutrient limitation, growth rate, methanogen

overall_design: Four biological replicates of hydrogen limited cells grown in chemostats were compared to four biological replicates of leucine limited and phosphate limited chemostat cultures. For growth rate comparisons, two sets were compared, each with three biological replicates of cultures grown at slow and rapid growth rates in chemostats. One set was limited by hydrogen availability at both growth rates, the other by phosphate availability. Each comparison was conducted with a dye swap and each contained two copies of the array, yielding 4 technical replicates for each biological replicate. This yielded a total of 16 replicates for the hydrogen versus leucine and hydrogen versus phosphate comparisons and 12 replicates each for the growth rate comparisons for both hydrogen and phosphate limitation. For growth rate comparisons under phosphate limited conditions a second scanning was done at lower gain set so that no spot reached saturation.

first: Erik

last: Hendrickson

first: Andrew

last: Haydock

first: Brian

last: Moore

first: William

last: Whitmann


title: MMP103

status: Public on Aug 30 2007

summary:
Methanococcus maripaludis is a methanogenic Archaea that conserves energy from molecular hydrogen to reduce carbon dioxide to methane. Chemostat grown cultures limited for phosphate or leucine were compared to determine the regulatory response to leucine limitation.
Keywords: archaea, hydrogen, leucine, phosphate, nutrient limitation, growth rate, methanogen

overall_design: Four biological replicates of leucine limited cells grown in chemostats were compared to four biological replicates of phosphate limited chemostat cultures. Each comparison was conducted with a dye swap and each contained two copies of the array, yielding 4 technical replicates for each biological replicate. This yielded a total of 16 replicates for the leucine versus phosphate comparisons.


title: Free fatty acids and TNF-alpha in hepg2/c3a cell culture

status: Public on Aug 04 2006

city: East Lansing

first: Zheng

last: Li

state: MI

address: 2527 Engineering Building

department: Chemical Engineering and Materials Science

institute: Michigan State University

summary:
free fatty acids(palmitate, oleate, linoleate) 0.7mM and tnf-alpha (0 20,100 ng/ml) were subjected to HepG2 cell line to study the cytotoxicity induced by these two factors
Keywords: stress response

overall_design:
control(Hepg2 medium and BSA medium)
treatment(combinations of TNFa+FFAs)
two biological replicates for each condition, color swap for each sample

first: Shireesh

last: Srivastava

first: Christina

last: Chan

first: Paul

last: Norton

first: James

last: Resau

last: Haab


title: LKB1 modulates lung cancer differentiation and metastasis

status: Public on Aug 28 2007

city: boston

first: kwok-kin

last: wong

address: 44 binney street

department: medical oncology

institute: dana farber cancer institute

summary:
Inherited mutation in LKB1 results in the Peutz-Jeghers syndrome (PJS), characterized by intestinal hamartomas and a modestly increased frequency of gastrointestinal and breast cancer1. Somatic inactivation of LKB1 occurs in human lung adenocarcinoma2-4, but its tumor suppressor role in this tissue is unknown.  Here we show that somatic Lkb1 deficiency strongly cooperates with somatic K-rasG12D activating mutation to accelerate the development of mouse lung tumorigenesis.  Lkb1 deficiency in the setting of K-rasG12D mutation (K-ras Lkb1L/L) was associated with decreased tumor latency and increased tumor aggressiveness including metastasis.  Furthermore, tumors from K-ras Lkb1L/L mice demonstrated histologies--squamous, adenosquamous and large cell--not seen with K-rasG12D mutation, Ink4a/Arf inactivation, or p53 inactivation alone or in combination.  Experiments in vitro suggest that LKB1 suppresses lung tumorigenesis and progression through both p16INK4a-ARF-p53 dependent and independent mechanisms.  These data indicate that LKB1 regulates lung tumor progression and differentiation.
Keywords: cancer research

sample_organism:
Homo sapiens
Mus musculus

overall_design: To analyze the role of LKB1 in lung cancer progression and differentiation, we have dissected the lung tumors from mice with/without lkb1 loss and performed the microarray analyses to compare their gene expression pattern. In addition, we have also performed microarray analysis in both A549 and H2126 cell lines after reconsistitution of either wt-lkb1 or the kinase dead form of lkb1 (lkb1-KD) to confirm what we observed from in vivo studies.

first: Hongbin

last: Ji

first: Matthew

middle: R

last: Ramsey

first: Neil

middle: D

last: Hayes

first: Cheng

last: Fan

first: Kate

last: McNamara

first: Piotr

last: Kozlowski

first: Chad

last: Torrice

first: Michael

last: Wu

first: Takeshi

last: Shimamura

first: Samanthi

last: Perera

first: Mei-Chih

last: Liang

first: Dongpo

last: Cai

first: George

last: Naumov

last: Bao

first: Cristina

last: Contreras

first: Danan

first: Liang

last: Chen

first: Janakiraman

last: Krishnamurthy

first: Jussi

last: Koivunen

first: Lucian

last: Chirieac

first: Robert

last: Padera

first: Roderick

last: Bronson

first: Neal

middle: I

last: Lindeman

first: David

last: Christiani

first: Xihong

last: Lin

first: Geoffrey

last: Shapiro

first: Pasi

last: Ja¨nne

first: Bruce

last: Johnson

last: Meyerson

last: Kwiatkowski

first: Diego

middle: H

last: Castrillon

first: Nabeel

last: Bardeesy

first: Norman

middle: E

last: Sharpless

first: Kwok-Kin

last: Wong


title: Chemokinetic versus Chemotactic Cancer Cells

status: Public on May 20 2006

city: Sydney

first: Lilian

last: Soon

state: NSW

address: LG14, Madsen Building, F09

department: Australian Key Centre for Microscopy and Microanalysis, EMU

country: Australia

institute: The University of Sydney

summary:
Background
Non-small cell lung cancer is the most common cause of early casualty from malignant disease in western countries. The heterogeneous nature of these cells has been identified by histochemical and microarray biomarker analyses. Unfortunately, the morphological, molecular and biological variation within cell lines used as models for invasion and metastasis are not well understood. In this study, we test the hypothesis that heterogeneous cancer cells exhibit variable motility responses such as chemokinesis and chemotaxis that can be characterized molecularly.
Methods
A subpopulation of H460 lung cancer cells called KINE that migrated under chemokinetic (no gradient) conditions was harvested from Boyden chambers and cultured.  Time-lapsed microscopy, immunofluorescence microscopy and microarray analyses were then carried out comparing chemokinetic KINE cells with the unselected CON cell population.
Results
Time-lapsed microscopy and analysis showed that KINE cells moved faster but less directionally than the unselected control population (CON), confirming their chemokinetic character.  Of note was that chemokinetic KINE cells also chemotaxed efficiently. KINE cells were less adhesive to substrate than CON cells and demonstrated loss of mature focal adhesions at the leading edge and the presence of non-focalized cortical actin.  These characteristics are common in highly motile amoeboid cells that may favour faster motility speeds.  KINE cells were also significantly more invasive compared to CON.  Gene array studies and real-time PCR showed the downregulation of a gene called, ROM, in highly chemokinetic KINE compared to mainly chemotactic CON cells.  ROM was also reduced in expression in a panel of lung cancer cell lines compared normal lung cells.
Conclusions
This study shows that cancer cells that are efficient in both chemokinesis and chemotaxis demonstrate high invasion levels.  These cells possess different morphological, cytoskeletal and adhesive properties from another population that are only efficient at chemotaxis, indicating a loss in polarity.  Understanding the regulation of polarity in the context of cell motility is important in order to improve control and inhibition of invasion and metastasis.
Keywords: Cancer cells, chemotaxis, chemokinesis, motility, gene regulation.


title: Human ovarian tumors and normal ovaries

status: Public on Apr 09 2007

city: Ann Arbor

first: Rork

last: Kuick

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary:
99 individual ovarian tumors (37 endometrioid, 41 serous, 13 mucinous, and 8 clear cell carcinomas) and 4 individual normal ovary samples, each assayed on an Affymetrix HG_U133A array
Keywords: Individual tumor comparisons

overall_design: 99 individual ovarian tumors (37 endometrioid, 41 serous, 13 mucinous, and 8 clear cell carcinomas) and 4 individual normal ovary samples.  RNA expression was analyzed using one Affymetrix HG_U133A array per sample.

first: Rong

last: Wu

first: Neali

last: Hendrix

last: Misek

first: Samir

middle: M

last: Hanash

first: Yali

last: Zhai

first: Donald

last: Schwartz

first: Aytekin

last: Akyol

first: Hidetaka

last: Katabushi

first: Bart

middle: O

last: Williams

first: Eric

last: Fearon

first: Kathleen

last: Cho


title: rre1 and rre2 mutants

status: Public on Sep 30 2005

city: Stanford

first: Shauna

last: Somerville

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution of Washington

summary:
Effect of chitin on rre-1 and rre-2 seedlings.
Keywords: other

first: Marta

last: Berrocal-Lobo

first: Bi-Huei

last: Hou


title: Comprehensive analysis of PPARa-dependent regulation of hepatic lipid metabolism by expression profiling

status: Public on Jul 24 2007

first: Guido

last: Hooiveld

institute: Wageningen University

summary:
PPARalpha is a ligand-activated transcription factor involved in the regulation of nutrient metabolism and inflammation. Although much is already known about the function of PPARalpha in hepatic lipid metabolism, many PPARalpha-dependent pathways and genes have yet to be discovered. In order to obtain an overview of PPARalpha-regulated genes relevant to lipid metabolism, and to probe for novel candidate PPARalpha target genes, livers from several animal studies in which PPARalpha was activated and/or disabled were analyzed by Affymetrix GeneChips. Numerous novel PPARalpha-regulated genes relevant to lipid metabolism were identified. Out of this set of genes, eight genes were singled out for study of PPARalpha-dependent regulation in mouse liver and in mouse, rat, and human primary hepatocytes, including thioredoxin interacting protein (Txnip), electron-transferring-flavoprotein beta polypeptide (Etfb), electron-transferring-flavoprotein dehydrogenase (Etfdh), phosphatidylcholine transfer protein (Pctp), endothelial lipase (EL, Lipg), adipose triglyceride lipase (Pnpla2), hormone-sensitive lipase (HSL, Lipe), and monoglyceride lipase (Mgll). Using an in silico screening approach, one or more PPAR response elements (PPREs) were identified in each of these genes. Regulation of Pnpla2, Lipe, and Mgll, which are involved in triglyceride hydrolysis, was studied under conditions of elevated hepatic lipids. In wild-type mice fed a high fat diet, the decrease in hepatic lipids following treatment with the PPARalpha agonist Wy14643 was paralleled by significant up-regulation of Pnpla2, Lipe, and Mgll, suggesting that induction of triglyceride hydrolysis may contribute to the anti-steatotic role of PPARalpha. Our study illustrates the power of transcriptional profiling to uncover novel PPARalpha-regulated genes and pathways in liver.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series

first: Maryam

last: Rakhshandehroo

first: Linda

last: Sanderson

first: Merja

last: Matilainen

first: Rinke

last: Stienstra

first: Carsten

last: Carlberg

first: Philip

last: de Groot

first: Michael

last: Muller

first: Sander

last: Kersten


title: Systemic inflammatory response syndrome and septic shock

status: Public on Apr 30 2006

city: Cincinnati

first: Hector

last: Wong

state: OH

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

summary:
Goal of the experiment:  To identify correlated genes, pathways and groups of patients with systemic inflammatory response syndrome and septic shock that is indicative of biologically important processes active in these patients.
Background:  We measured gene expression levels and profiles of children with systemic inflammatory response syndrome (SIRS) and septic shock as a means for discovering patient sub-groups and gene signatures that are active in disease-affected individuals and potentially in patients with poor outcomes.
Methods:  Microarray and bioinformatics analyses of 123 microarray chips representing whole blood derived RNA from controls, children with SIRS, and children with septic shock.
Results:  A discovery-based filtering approach was undertaken to identify genes whose expression levels were altered in patients with SIRS or septic shock. Clustering of these genes identified 3 Major and several minor sub-groups of patients with SIRS or septic shock. The three groups differed with respect to incidence of septic shock and trended toward differences in mortality. Statistical analyses demonstrated that 6,435 gene probes were differentially regulated between the three patient sub-groups (false discovery rate < 0.001%). Of these gene probes, 623 gene probes within 7 major gene ontologies accounted for the majority of group differentiation. Network analyses of these 623 gene probes demonstrated 5 major gene networks that were differentially expressed between the 3 groups. Statistical comparison of septic shock survivors and non-survivors identified one major gene network that was under expressed in a high fraction of the non-survivors and identified potential biomarkers for poor outcome.
Conclusions:  This is the first genome-level demonstration of pediatric patient sub-groups with SIRS and septic shock. The sub-groups differ clinically and differentially express 5 major gene networks. We have identified gene signatures and potential biomarkers associated with poor outcome in children with septic shock. These data represent a major advancement in our genome-level understanding of pediatric SIRS and septic shock.
Keywords: Septic shock, SIRS, pediatrics, outcome, infection, inflammation

overall_design:
Children < 10 years of age admitted to the pediatric intensive care unit and meeting the criteria for either SIRS or septic shock were eligible for the study. SIRS and septic shock were defined based on pediatric-specific criteria. We did not use separate categories of "sepsis" or "severe sepsis". Patients meeting criteria for "sepsis" or "severe sepsis" were placed in the categories of SIRS and septic shock, respectively, for study purposes. Control patients were recruited from the outpatient or inpatient departments of the participating institutions using the following exclusion criteria:  a recent febrile illness (within 2 weeks), recent use of anti-inflammatory medications (within 2 weeks), or any history of chronic or acute disease associated with inflammation.
After obtaining informed consent, blood samples were obtained on Day 1 of the study, and when possible on Day 3 of the study. Blood samples were divided for RNA extraction and isolation of serum. Severity of illness was calculated based on the PRISM III score. Organ failure was defined based on pediatric-specific criteria. Annotated clinical and laboratory data were collected daily while in the intensive care unit. Study patients were placed in the study categories of SIRS or Septic Shock on Day 1 of the study. On Day 3 of the study, patients were classified as SIRS, Septic Shock, or SIRS resolved (no longer meeting criteria for SIRS). All study patients were followed for 28 days to determine mortality or survival. Clinical, laboratory, and biological data were entered and stored using a web-based data base developed locally.

first: Thomas

middle: P

last: Stanley

first: Bhuvaneswari

last: Sakthivel

first: Natalie

last: Cvijanovich

first: Richard

last: Lin

first: Geoff

last: Allen

first: Neal

last: Thomas

first: Allan

last: Doctor

first: Meena

last: Kalyanaraman

first: Nancy

last: Tofil

first: Scott

last: Penfil

first: Marie

last: Monaco

first: Mary-Ann

last: Tagavilla

first: Kelli

last: Odoms

first: Bruce

last: Aronow


title: Regulation of gene networks in photoperception-related functions by the CRX/OTX homologue Otd in Drosophila

status: Public on Apr 30 2007

city: Boston

first: Francesca

last: Pignoni

address: 243 Charles Street

department: Department of Ophthalmology

institute: Harvard Medical School and Massachusetts Eye and Ear Infirmary

summary:
Comparative global gene expression analysis was caried out using pupal head tissue of otd-uvi an eye specific mutant allele of Otd and wild type control Canton S., in order to delineate the function of homeobox transcription factor Otd in Drosophila photoreceptor development and function.
Keywords: genetic modification

overall_design: The Drosophila strain Canton S was used as wild type for comparative gene expression analysis with the mutant strain otd-uvi.  For each biological replicate, samples were derived from independent RNA extractions consisting of 15-20 pupal heads. Pupae were dissected at 80 hr APF and immediately transferred to 600ul of trizol (GIBCO/BRL). RNA extraction was performed according to manufacturers instructions. Qualitative and quantitative analysis of the total RNA was carried out by capillary electrophoresis on a RNA6000 Nano Assay chip, with Agilent 2100 Bioanalyzer (Agilent Technologies USA) Biotin labeled probes were generated from 10ug total RNA according to Affymetrix protocol.

first: Swati

middle: S

last: Ranade

first: Donghui

last: Yang-Zhou

first: Sek-Won

last: Kong


title: SHR kidney

status: Public on Apr 01 2005

city: Houston

first: Peter

last: Doris

state: TX

institute: University of Texas HSC Houston

summary:
Affymetrix RG U34A analysis of renal gene expression in Wistar-derived rat strains
Keywords: repeat sample

first: Cruz

last: Hinojos


title: Egg quality after natural and controlled ovulation

status: Public on Oct 03 2006

city: Rennes

first: Julien

last: Bobe

institute: Institut National de la Recherche Agronomique

summary:
The present study aimed at studying the rainbow trout egg transcriptome using 9152-cDNA microarrays after natural or controlled ovulation. The analysis of egg transcriptome after natural or controlled ovulation led to the identification of 26 genes. We observed that both hormonal induction and photoperiod control of ovulation induced significant changes in the egg mRNA abundance of specific genes.
We demonstrate that hormonal induction of ovulation has an impact on the egg mRNA abundance of specific genes even though the resulting effects on the developmental potential of the egg is so far unknown.
In addition, we also identified 1 gene exhibiting a differential mRNA abundance in eggs of varying developmental potential.
Keywords: Egg quality-dependent

overall_design: Analysis of egg transcriptome after natural ovulation (4 samples), photoperiod-controlled ovulation (14 samples), and hormonally-induced ovulation (11 samples).

first: Emilie

last: Bonnet

first: Alexis

last: Fostier


title: Rat Chondrosarcoma

status: Public on Jul 24 2004

city: Iowa City

first: Thomas

middle: L.

last: Casavant

state: IA

department: Electrical & Computer Department

institute: University of Iowa

summary:
These libraries represent instances of Swarm rat chondrosarcoma tumors  taken from different transplantation experiments.  This series also  contains one non-cancerous cartilage library made from rat normal  growing femoral head cartilage as a comparative data point.
Keywords: other

first: Chris

last: Hamm

first: Jeff

last: Stevens

first: Hakeem

last: Almabrazi

first: Todd

last: Scheetz

first: Tom

first: M

middle: B

last: Soares


title: IFNb induced genes in MEFs

status: Public on Dec 31 2005

city: Memphis

first: Lawrence

last: Pfeffer

state: TN

address: 930 Madison Avenue,#530

department: Pathology

institute: University of Tennessee Health Science

summary:
A number of IFN-induced proteins are believed to be responsible for the antiviral state induced by IFNs. Our microarray analysis of IFN-regulated genes in MEFs from wild-type mice identified 124 probe sets that were differentially regulated upon IFN treatment. This group consisted of many known ISGs such as Ifit1, Gbp2, mx1, Isg15, Stat1, nmi, mx2, If204, Adar, Irf1, and protein kinase R.
Keywords: repeat

overall_design: 3 control and 3 IFNb-treated biological replicates were analyzed

first: Ramin

last: Homayouni

first: Lai

last: Wei


title: Gene expression of breast cancer tissue in a large population-based cohort of Swedish patients

status: Public on May 31 2006

city: Stockholm

first: Alexander

last: Ploner

department: Medical Epidemiology and Biostatistics

country: Sweden

institute: Karolinska Institutet

summary:
Tissue material was collected from all breast cancer patients receiving surgery at Karolinska Hospital from 1994-1996. Material was frozen immediatley on dry ice or in liquid nitrogen and stored in -70°C freezers. This series contains expression data for n=159 tumors from which RNA could be collected in sufficient amounts and quality for analysis.
Keywords: breast cancer, expression profiling, predictive gene signature, molecular classification of cancecr

overall_design: All tumor specimens were assessed on U133 A and B arrays.

first: Yudi

last: Pawitan

first: Judith

last: Bjohle

first: Lukas

last: Amler

first: Anna-Lena

last: Borg

first: Suzanne

last: Egyhazi

first: Per

last: Hall

first: Xia

last: Han

first: Lars

last: Holmberg

first: Fei

last: Huang

first: Sigrid

last: Klaar

first: Edison

middle: T

last: Liu

first: Lance

last: Miller

first: Hans

last: Nordgren

first: Kerstin

last: Sandelin

last: Shaw

first: Johanna

last: Smeds

first: Lambert

last: Skoog

first: Sara

last: Wedren

first: Jonas

last: Bergh


title: Transcript analysis of aluminum tolerance responses in Medicago truncatula

status: Public on Feb 08 2007

city: St Paul

first: Kathryn

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

institute: University of Minnesota

summary:
For transcript analysis of aluminum tolerance responses in Medicago truncatula we compared transcripts from 2.5 µM Al-treated and control (-Al) root tips corresponding to 12 and 48 h after Al treatment in Al-tolerant (T32) and Al-sensitive (S70) lines.
Keywords: 2 time points and 2 lines

overall_design:
Time course of 2 time points and 2 lines consists of 24 microarrays.
Each time point experiment consists of three direct (reps1, 2, 3) and three dye-swapped (reps 4, 5, 6) technical replicates.

first: Divya

last: Chandran

first: Natasha

last: Sharopova

first: Deborah

last: Samac


title: Normal and transformed human mature B cells

status: Public on Apr 04 2005

city: New York

first: Katia

last: Basso

state: NY

address: 1150 St. Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

summary: Phenotypes representative of normal, transformed and experimentally manipulated human B cells related to the germinal center structure.


title: Preovulatory ovary

status: Public on Jun 08 2006

first: Julien

last: Bobe

address: Campus de Beaulieu

summary:
Nylon microarrays displaying 9152 rainbow trout cDNAs were hybridized using RNA samples originating from ovarian tissue collected during late vitellogenesis, post-vitellogenesis and oocyte maturation. Differentially expressed genes were identified using a statistical analysis. A supervised clustering analysis was performed using only differentially expressed genes in order to identify gene clusters exhibiting similar expression profiles. In addition, specific genes were selected and their preovulatory ovarian expression was analyzed using real-time PCR.
From the statistical analysis, 310 differentially expressed genes were identified. Among those genes, 90 were up-regulated at the time of oocyte maturation while 220 exhibited an opposite pattern. After clustering analysis, 90 clones belonging to 3 gene clusters exhibiting the most remarkable expression patterns were kept for further analysis. Using real-time PCR analysis, we observed a strong up-regulation of ion and water transport genes such as aquaporin 4 (aqp4) and pendrin (slc26). In addition, a dramatic up-regulation of vasotocin (avt) gene was observed. Furthermore, angiotensin-converting-enzyme 2 (ace2), coagulation factor V (cf5), adam 22, and the chemokine cxcl14 genes exhibited a sharp up-regulation at the time of oocyte maturation. Finally, ovarian aromatase (cyp19a1) exhibited a dramatic down-regulation over the post-vitellogenic period while a down-regulation of Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (cmah) was observed at the time of oocyte maturation.
We showed the over or under expression of more that 300 genes, most of them being previously unstudied or unknown in the fish preovulatory ovary. Our data confirmed the down-regulation of estrogen synthesis genes during the preovulatory period. In addition, the strong up-regulation of aqp4 and slc26 genes prior to ovulation suggests their participation in the oocyte hydration process occurring at that time. Furthermore, among the most up-regulated clones, several genes such as cxcl14, ace2, adam22, cf5 have pro-inflammatory, vasodilatory, proteolytics and coagulatory functions. The identity and expression patterns of those genes support the theory comparing ovulation to an inflammatory-like reaction.
Keywords: ovarian stages comparisons

overall_design:
Late vitellogenesis: 3 samples
Post-vitellogenesis: 4 samples
Oocyte maturation (germinal vesicle breakdown): 6 samples

first: Jerome

last: Montfort

first: Thaovi

last: Nguyen

first: Alexis

last: Fostier


title: Kidney expression

status: Public on Sep 09 2003

city: Cleveland

first: Michael

last: Simonson

address: 2109 Adelbert Rd

department: Medicine- Nephrology

institute: Case Western Reserve University

summary:
RNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA.
Keywords: other

first: Rangnath

last: Mishra


title: Prostate Cancer

status: Public on Dec 30 2005

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Prostate cancer, a leading cause of cancer death, displays a broad range of clinical behavior from relatively indolent to aggressive metastatic disease. To explore potential molecular variation underlying this clinical heterogeneity, we profiled gene expression in 62 primary prostate tumors, as well as 41 normal prostate specimens and nine lymph node metastases, using cDNA microarrays containing approximately 26,000 genes. Unsupervised hierarchical clustering readily distinguished tumors from normal samples, and further identified three subclasses of prostate tumors based on distinct patterns of gene expression. High-grade and advanced stage tumors, as well as tumors associated with recurrence, were disproportionately represented among two of the three subtypes, one of which also included most lymph node metastases. To further characterize the clinical relevance of tumor subtypes, we evaluated as surrogate markers two genes differentially expressed among tumor subgroups by using immunohistochemistry on tissue microarrays representing an independent set of 225 prostate tumors. Positive staining for MUC1, a gene highly expressed in the subgroups with "aggressive" clinicopathological features, was associated with an elevated risk of recurrence (P = 0.003), whereas strong staining for AZGP1, a gene highly expressed in the other subgroup, was associated with a decreased risk of recurrence (P = 0.0008). In multivariate analysis, MUC1 and AZGP1 staining were strong predictors of tumor recurrence independent of tumor grade, stage, and preoperative prostate-specific antigen levels. Our results suggest that prostate tumors can be usefully classified according to their gene expression patterns, and these tumor subtypes may provide a basis for improved prognostication and treatment stratification.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

overall_design: Using regression correlation

first: Jacques

last: Lapointe


title: Sodium butyrate induced gene expression changes in the Madin-Darby bovine kidney epithelial cells

status: Public on Jan 05 2006

city: Beltsville

first: Robert

middle: W

last: Li

state: MD

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

summary:
The Madin-Darby bovine kidney epithelial cells, when at approximately 50% confluence (during the exponential phase), were treated with 10mM sodium butyrate for 24h.  Butyrate induced profound changes in gene expression related with multiple signal transduction pathways such as cell cycle control, apoptosis and extracellular matrix remodeling in this cell line
Keywords: stress response, two class unpaired design

overall_design: Six single channel hybridizations were performed (treated vs control), 3 replicates each.

first: Cong-Jun