title: Therapeutic use of microRNA-181a in the adoptive immunotherapy of cancer

first: Nicholas

last: Restifo

address: CRC Room 3-5762

institute: NCI

summary:
The generation of highly-reactive T lymphocytes against tumor-associated antigens remains an obstacle for effective adoptive immunotherapy of cancer. Recently, we found that microRNA-181a (miR-181a) acts as an intrinsic modulator of T cell antigen sensitivity in a transgenic T cell line in vitro. This molecule is part of a growing family of evolutionarily selected small interfering RNA that control gene expression at the posttranscriptional level by targeting messenger RNA (mRNA) for degradation or translational repression. Here, we explored the use of miR-181a to improve anti-tumor T cell responsiveness against weakly immunogenic tumor-associated antigens. We found that genetic engineering of T lymphocytes with miR-181a dramatically augmented the function of poorly responsive human tumor-infiltrating lymphocytes and TCR-engineered peripheral blood lymphocytes, resulting in potent anti-tumor reactivity. Furthermore, in a mouse model, miR-181a increased the function of self/tumor-specific CD8+ T cells enabling effective tumor destruction in the absence of vaccination or exogenous cytokines that were otherwise essential requirements and thus represents a significant advance over previous approaches. Although miRNAs have been previously shown to play critical functional roles in the development and function of vertebrate immune systems and pathogenesis of cancer, this report comprises the first use of a miRNA gene as tool in the treatment of disease.
Keywords: cellular modification design

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For the 6 mouse samples the Operon Array-Ready Oligo Set (AROS™) V 4.0 contains 35,852 longmer probes representing 25,000 genes and about 38,000 gene transcripts and also includes 380 controls platform was used and each sample was hybridized in duplicate. For the 6 human samples, the human cDNA microarray platform was used which consist of 17 k cDNA array included a combination from a RG_HsKG_031901 7 k clone set and 10,000 clones from the RG_Hs_seq_ver_070700 40 k clone set (Research Genetics, Huntsville, AL). The cDNA clones include 12,072 uniquely named genes, 875 duplicates of named genes.


title: wt/myb77-Functional characterization of AtMYB77 transcription factor.

status: Public on Aug 13 2008

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

department: URGV

country: France

institute: INRA

summary:
au07-03_myb77 - wt/myb77 - Transcriptome analysis of Myb77 knock out mutant line or of Myb77fragment overxpressing transgenic line. - Plants were grown in vitro on 1/2 MS medium, 3% sucrose, 0.8% agar for 21 days under balance day cycle (12 hours daylight at 22°C; 12 hours dark at 20°C) in climate chamber. The whole plants were collected for RNAs extraction.
Keywords: gene knock in (transgenic),gene knock out

overall_design: 4 dye-swap - CATMA arrays

first: Jean-Pierre

middle: P

last: Renou

first: Udo

last: Conrad

first: My-Linh

middle: L

last: Tran

first: Marie-Laure

last: Martin-Magniette


title: Mucosal Glycan Foraging Enhances the Fitness and Transmission of a Saccharolytic Human Distal Gut Symbiont

status: Public on Nov 21 2008

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

state: MI

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

country: USA

institute: University of Michigan Medical School

summary: Gene expression profiles of Bacteroides thetaiotaomicron in vitro during growth on host mucosal polysaccharides as sole carbon sources. All substrates in this series are derived from porcine gastric mucin and include mucin O-glycans and glycosaminoglycans.

platform_organism:
Bacteroides thetaiotaomicron
Bifidobacterium longum

overall_design: Two different culture formats used: 800ml batch-culture bioreactors and 5ml tube cultures (format is indicated within each sample title). Each set of growths was referenced to a minimal medium glucose reference corressponding to the same culture format. Unfractionated porcine mucosal glycan (PMG) growths were compared to previously published in vivo datasets, which were referenced to the 800ml minimal medium glucose reference dataset.

middle: C

first: Herbert

last: Chiang

first: Jeffrey

middle: I

last: Gordon


title: DEN-induced HCC in c-Met knockout mice

status: Public on Aug 09 2008

city: Bethesda

first: Snorri

middle: S

last: Thorgeirsson

state: MD

address: 37 Convent Dr. # 4146

department: Cellular and Molecular Biology Section

institute: National Cancer institute/NIH

summary:
HGF has been reported to have both positive and negative effects on carcinogenesis. Here we show that the loss of c-Met signaling in hepatocytes enhanced rather than suppressed the early stages of chemical hepatocarcinogenesis. c-Met conditional knockout mice (c-metfl/fl, AlbCre+/-; MetLivKO) treated with N-nitrosodiethylamine (DEN) developed significantly more and bigger tumors and with a shorter latency as compared with control (wt/wt, AlbCre+/-; Cre-Ctrl) mice. Accelerated tumor development was associated with increased rate of cell proliferation and prolonged activation of epidermal growth factor receptor (EGFR) signaling. MetLivKO livers treated with DEN also displayed elevated lipid peroxidation, decreased ratio of reduced glutathione (GSH) to oxidized glutathione (GSSG), and upregulation of superoxide dismutase 1 (Sod1) and heat shock protein 70 (Hsp70), all consistent with increased oxidative stress. Likewise, gene expression profiling performed at 3 and 5 months after DEN treatment revealed upregulation of genes associated with cell proliferation and stress responses in c-Met mutant livers. The negative effects of c-Met-deficiency were reversed by chronic oral administration of anti-oxidant N-acetylcysteine (NAC). NAC blocked the EGFR activation and reduced the DEN-initiated hepatocarcinogenesis to the levels of Cre-Ctrl mice. These results argue that intact HGF/c-Met signaling is essential for maintaining normal redox homeostasis in the liver and has tumor suppressor effect(s) during the early stages of DEN-induced hepatocarcinogenesis.
Keywords: compound treatment design

overall_design: To address a role for c-Met in liver carcinogenesis, we employed a hepatocyte specific c-Met conditional knockout mouse model generated in our laboratory. Mice received a single intraperitoneal injection of 10 µg/g body weight of N-nitrosodiethylamine (DEN) (Sigma-Aldrich, Inc., St. Louis, MO, USA) at 14 days of age. Livers were examined at 3 and 5 months after DEN injection. Expression profiling was conducted on five animals from each genotype per time point. Total RNA pooled from five wild-type B6/129 strain mouse livers was used as universal hybridization reference. All experiments were performed in duplicates following a dye-swapping design. Arrays were scanned with a GenePix 4000A scanner (Axon Instruments Ltd., Burlingame, CA) in a way to achieve optimal signal intensity at both channels with less than 1% saturated spots. After excluding the invalid features, all arrays were normalized to the 50th percentile of the median signal intensity using the mAdb data analysis suite (http://nciarray.nci.nih.gov/). Unsupervised cluster analysis was performed with the Cluster and TreeView programs (http://rana.lbl.gov/EisenSoftware.htm). The BRB ArrayTools V3.3.0 software package (Biometric Research Branch, National Cancer Institute; http://linus.nci.nih.gov/BRB-ArrayTools.html) was used for the supervised comparison. Differentially expressed genes were selected using a univariate 2-sample t-test (P<0.001) with a random variance model (15). Functional classification of the significant genes was based on the Gene Ontology (GO) annotations (www.geneontology.org).


title: rfppr-Comparing nuclear gene expression in two CMS-systems using microarray technology

status: Public on Aug 01 2008

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

summary:
ra05-11_cmsrapeseed - rfppr - -To understand how/if fertility and the mitochondrial background are interlinked. -To understand how the mitochondrial background influences the nuclear gene expression. -Compare and describe the total nuclear gene expression of CMS vs. fertile and CMS vs. Restored. -Describe and analyse genes that differ in expression (of special interest are genes that differs in both comparisons). -Group genes e.g. floral genes, highly expressed genes, transcription factors, nuclear encoded genes targeted for the mitochondrion. -Comparing two CMS-systems to elucidate differences and similarities between them.  - Flower buds from three B. napus lines (Pactol, CMS, Rfo PPR) at one developmental stage (stage 8).
Keywords: wt vs mutant comparison

overall_design: 6 dye-swap - CATMA arrays

first: Francoise

last: Budar


title: mir398 mutant analysis-Analysis of miR398 mutants.

status: Public on Jul 11 2008

summary:
adt07-03_mir398-mutants - mir398 mutant analysis - Defining new targets of miR398 by transcriptome analysis of two miR398 mutant alleles. - Plants were grown on soil in culture chambers under the following conditions, a day/night cycle of 16/8 hours was applied, light intensity was around 100-150 umol m-2 s-1, temperature day/night was 20/15°C. Plants were harvested 17 days later and RNAs were then extracted. The experiment was repeated twice.
Keywords: gene knock out

first: Nicolas

last: Bouche


title: dspa/e of erwinia amylovora-Regulation of the Arabidopsis transcriptome by the type three effector DspA/E of E...

status: Public on Jul 10 2008

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

summary:
ra06-03_dspa-erwinia - dspa/e of erwinia amylovora - Identification of Arabidopsis genes regulated by the type three effector Dspa/E of Erwinia amylovora. - Regulation of the Arabidopsis transcriptome by the type three effector DspA/E of Erwinia amylovora. 5-week old Arabidopsis plants were leaf infiltrated with Erwinia amylovora wild-type (wt), type three secretion mutant (sec) or dspA/E mutant (dspA/E) strains.
Keywords: wt vs mutant comparison

first: Ludivine

last: Taconnat

first: Mathilde

last: Fagard


title: Tumor-specific Th17-polarized cells eradicate large established melanoma

status: Public on Mar 15 2008

first: Keith

last: Kerstann

department: Surgery Branch

institute: National Institutes of Health

summary:
CD4+ T cells can differentiate into multiple effector subsets but the potential roles of these subsets in anti-tumor immunity have not been fully explored. We sought to study the impact of CD4+ T cell polarization on efficacy of tumor rejection in a model closely mimicking human disease where the target antigens are often non-mutated tissue differentiation self-antigens. We generated a new transgenic mouse model in which CD4+ T cells recognize a novel epitope in tyrosinase-related protein 1 (TRP-1), an antigen that is expressed by normal melanocytes and B16 murine melanoma. We found that cells could be robustly polarized into Th0, Th1 and Th17 subtypes in vitro, as evidenced by cytokine, chemokine, and adhesion molecule profiles as well as by surface markers, suggesting the potential for differential effector function in vivo. Contrary to the current view that Th1 cells play the most important role in tumor rejection, we found that Th17-polarized cells were superior in mediating destruction of advanced B16 melanoma. Unexpectedly, their therapeutic effect was critically dependent on IFN-γ production, while depletion of IL-17A and IL-23 had little impact. Taken together, these data indicate that the appropriate in vitro polarization of effector CD4+ T cells is decisive for the successful tumor eradication. This principle should be taken under consideration in the design of future clinical trials involving adoptive transfer-based immunotherapy of human malignancies.
Two-condition experiment:  RNA from TRP-1 transgenic mouse lymphocytes polarized to be either Th1 or Th17 were compared to cells polarized to be Th0.
Keywords: Lymphocyte polarization comparison

overall_design: Comparative analysis of gene expression changes observed when murine lymphocytes are differentially in vitro polarized .

middle: W

first: Pawel

last: Muranski


title: nrt2.4-NRT2.4 NO3 transport mutant.

status: Public on Mar 12 2008

summary:
ra04-04_nrt2.4 - nrt2.4 - Transcriptome of the AtNRT2.4 mutant - Mutants have no phenotype
Keywords: gene knock out

overall_design: 2 dye-swap - CATMA arrays

last: Vedele

first: Frank

last: Chopin


title: maternal/embryonic aba-1-Analysis of the role of maternal and embryonic ABA in seeds.

status: Public on May 29 2008

first: Agnes

last: Yu

summary:
ra07-02_aba2 - maternal/embryonic aba-1 - Identification of genes regulated by maternal and embryonic ABA - Comparison of expression in seeds (15 days after pollination) of aba2-2 mutant to wild type (Col-0), aba2 (female) x Col-0 (male) crossing, and aba2-2 sprayed with ABA (100 micro M, twice a week).
Keywords: gene knock out,treated vs untreated comparison

first: Jean-Pierre

last: Renou

first: Annie

last: Marion-poll


title: cms4:19 and at chr3-Comparing nuclear gene expression in two CMS-systems using microarray technology

summary:
ra05-11_cmsrapeseed - cms4:19 and at chr3 - -To understand how/if fertility and the mitochondrial background are interlinked. -To understand how the mitochondrial background influences the nuclear gene expression. -Compare and describe the total nuclear gene expression of CMS vs. fertile and CMS vs. Restored. -Describe and analyse genes that differ in expression (of special interest are genes that differs in both comparisons). -Group genes e.g. floral genes, highly expressed genes, transcription factors, nuclear encoded genes targeted for the mitochondrion. -Comparing two CMS-systems to elucidate differences and similarities between them.  - Flower buds from four different B. napus lines (fertile cv Hanna, CMS-line 4:19, restored line 46, cv Hanna with the additon of A. thaliana chr 3) at two developmental stages (stages 0-5 and stage 8).
Keywords: wt vs mutant comparison

overall_design: 16 dye-swap - CATMA arrays

first: Marie-Laure

last: Martin-Magniette


title: fwa-leaves-Effect of DNA hypomethylation on gene expression

summary:
au05-02_fwa - fwa-leaves - Which gene are upregulated in a hypomethylated mutant? - Compare gene expression between WT leaves and hypomethylated leaves
Keywords: gene knock out

overall_design: 5 dye-swap - CATMA arrays

first: Frederic

last: Berger


title: fwa-pollen-Effect of DNA hypomethylation on gene expression

status: Public on Jun 07 2008

summary:
au05-02_fwa - fwa-pollen - Which gene are upregulated in a hypomethylated mutant? - Compare gene expression between WT pollen and mutant pollen
Keywords: gene knock out


title: stifenia-Effects of Stifenia pretreatment on Arabidopsis thaliana resistance against Fusarium oxysporum pv rafani

summary:
ra05-07_stifenia - stifenia - Does Stifenia elicitor pretreatment prime defense genes? - Stifenia sprayed and/or Fusarium infection.
Keywords: treated vs untreated comparison

first: Jean-Claude

last: Baccou


title: IL-2 and IL-21 confer opposing differentiation programs to CD8+ T cells for adoptive immunotherapy

status: Public on Feb 13 2008

summary:
IL-2 and IL-21 are closely related cytokines that might have arisen by gene duplication. Both cytokines promote the function of effector CD8+ T cells, but their distinct effects on antigen-driven differentiation of naïve CD8+ T cells into effector CD8+ T cells are not clearly understood. We found that antigen-induced expression of eomesodermin and maturation of naïve CD8+ T cells into granzyme B and CD44 expressing effector CD8+ T cells was enhanced by IL-2, but, unexpectedly, suppressed by IL-21. Furthermore, IL-21 repressed expression of IL-2Ra and inhibited IL-2-mediated acquisition of a cytolytic CD8+ T cell phenotype. Despite its inhibitory effects, IL-21 did not induce anergy, but instead potently enhanced the capacity of cells to mediate tumor regression upon adoptive transfer. In contrast, IL-2, surprisingly, impaired the subsequent anti-tumor function of transferred cells. Gene expression studies revealed a distinct IL-21-program that was characterized phenotypically by increased expression of L-selectin and functionally by enhanced anti-tumor immunity that was not reversed by secondary in vitro stimulation with antigen and IL-2. Thus, the efficacy of CD8+ T cells for adoptive immunotherapy can be influenced by opposing differentiation programs conferred by IL-2 and IL-21, a finding with important implications for the development of cellular cancer therapies.
Two-condition experiment:  Cytokine-exposed t-cells subsequentially restimulated without cytokine vs. control t-cells without cytokine subsquentially restimulated without cytokine. 3 independent experiments - 1 with experimental RNA labeled with Cy5, control with Cy3, and 2 with dyes-swapped
Keywords: Cytokine exposure comparison

overall_design:
Comparitive analysis of cytokine effects on lymphocyte gene expression.

GSM265712.gpr (S89_1_IL2_0.gpr): Cy3 - control, Cy5 - experimental
GSM265713.gpr (S90_1_IL15_0.gpr): Cy3 - control, Cy5 - experimental
GSM265714.gpr (S91_1_IL21_0.gpr): Cy3 - control, Cy5 - experimental
GSM265715.gpr (S27_2_0_IL2.gpr): Cy3 - experimental, Cy5 - control
GSM265716.gpr (S29_2_0_IL15.gpr): Cy3 - experimental, Cy5 - control
GSM265717.gpr (S30_2_0_IL21.gpr): Cy3 - experimental, Cy5 - control
GSM265718.gpr (S31_3_0_IL2.gpr): Cy3 - experimental, Cy5 - control
GSM265719.gpr (S33_3_0_IL15.gpr): Cy3 - experimental, Cy5 - control

first: Christian

last: Hinrichs


title: analysis of npc48 overexpressing plants-Analysis of npc48 overexpressing plants.

status: Public on Apr 12 2008

summary:
rs07-02_npc48 - analysis of npc48 overexpressing plants - Identification of potential targets of the non-protein codding RNA npc48. - We have lines overexpressing npc48 that shhowed a leaf morphological phenotype (serrated leaves). The proportion of lines havin gthe phenotype is around 20% of total transformants. We wanted to compare the transcriiptome of npc48-overexpressing lines with and without phenotype together with a transformation control for an additional control.
Keywords: gene knock in (transgenic)

first: Martin

last: Crespi


title: atnar2.1-1-Atnar2.1-1 response to transfer on low nitrate condition

first: Frederique

last: Bitton

summary:
ra05-12_nar2 - atnar2.1-1 - Does the ko of AtNAR2.1 leads to a differential expression in comparison to the WT when grown under high nitrate condition and transfered onto low nitrate concentration? - Plants were grown for 41 days in hydroponics in media containing 6 mM nitrate and then transferred to 6 or 0.2 mM nitrate media for 24h ( short days, irradiation 150 uE). Plants were harvested on day 42 during the first 2 hours of light.
Keywords: dose response,gene knock out

overall_design: 8 dye-swap - CATMA arrays

first: Anne

last: Krapp

last: Orsel


title: aba4/1-Analyse of arabidopsis mutants and transforming affected in the synthesis of abscissic acid.

status: Public on May 20 2008

last: Ludivine

summary:
ra07-03_aba4 - aba4/1 - Identification of genes deregulated in aba4 mutant or overexpressers. - Comparison of different genotypes to wild type Col-0: aba4-3 mutant, two independent 35S-ABA4 transgenic lines and two independent 35S-NCED6 transgenic lines.
Keywords: gene knock in (transgenic),gene knock out

last: Taconnat


title: F. verticillioides cultures on dissected maize tissues

status: Public on Dec 31 2007

city: Peoria

first: Robert

last: Butchko

state: IL

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

summary:
F. verticillioides cultured on dissected maize tissues.
Keywords: Differential gene expression

overall_design: Wild type F. verticillioides strain 7600 cultured for four days on different maize tissues.

first: Charles

last: Woloshuk

middle: A

first: Burton

middle: H

last: Bluhm


title: Clubroot catma-2: Deciphering the Arabidopsis mechanisms of resistance to clubroot (Plasmodiophora brassicae)

status: Public on Feb 09 2008

first: Soubigou-Taconnat

summary:
ra03-05_clubroot - clubroot catma-2 - Characterisation of the transcriptional changes (host genes up- and down-regulated) during the P. brassicae / A. thaliana interaction. - The objective was to identify the genes up and down-regulated between susceptible and partially resistant plants. The Arabidopsis accession Bur-0 shows partial resistance against the isolate eH of P. brassicae, whereas it is susceptible against the isolate e2. The transcriptome patterns of Bur-0 plants inoculated either by isolate e2 or isolate eH were compared at one week after inoculation. A similar comparison was done on roots. The entire experiment was repeated (biological repetition) and each comparison was performed in two independent hybridisations (technical repetition).
Keywords: organ comparison

first: Ludivine

first: Maria

last: Manzanares


title: Gene expression of Bacteroides thetaiotaomicron, in vivo with and without IgA 225.4

status: Public on Dec 27 2007

city: St Louis

first: Daniel

last: Peterson

state: MO

address: 4444 Forest Park

department: Molecular Biology and Pharmacology

institute: Center for Genome Sciences

summary:
Rag1-/- C57BL/6  or Rag1-/- C57BL/6 injected with the IgA producing hybridoma producing 225.4 anti- Bacteroides thetaiotaomicron (Capsular polysaccharide 4 dependent carbohydrate epitope specific epitope) mice were colonized with B. thetaiotaomicron wildtype strain VPI-5482 for 10 days.  Cecal bacteria were harvested and snap frozen and RNA isolated.
Keywords: Single time point, experimental and control groups.

overall_design: There are 4 replicates of mice with no IgA (Rag1 - Rag 4) and 4 replicates of mice with the 225.4 IgA (Backpack1 -Backpack4)

first: Jeffrey

last: IGordon


title: The impact of cell wall alterations on global gene expression. Comparative analysis of mutant.

status: Public on Nov 07 2007

summary:
Comparison of drv1 mutant against wild type in stems
Keywords: gene knock out

overall_design: 1 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Deborah

last: Goffner


title: Drosophila pole cell transcriptome in early embryogenesis (stage 4).

status: Public on Dec 10 2007

city: Okazaki

first: Shuji

last: Shigenobu

state: Aichi

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

summary:
To screen transcripts enriched in pole cells, primordial germ cells of Drosophila, during early embryogenesis, we compared transcriptome between pole cells and whole embryos at stage 4 by a microarray analysis. We used fluorescence-activated cell sorting (FACS) to isolate pole cells from the embryos carrying the transgene, EGFP-vasa, which expresses GFP specifically and continuously in the germline throughout the life cycle.
Keywords: cell type comparison

overall_design: RNA from FACS-sorted pole cells and from the whole embryos were hybridized to a microrray after Cy3/Cy5 labeling. Dye-swap experiment was carried out.

first: Jun

last: Yatsu

first: Makoto

last: Hayashi

first: Kayo

last: Arita

first: Satoru

last: Kobayashi


title: Rhodococcus sp. RHA1 grown on propane versus pyruvate

status: Public on Nov 01 2007

city: Vancouver

first: Justin

middle: Christian

last: LeBlanc

state: British Columbia

address: 2350 Health Sciences Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

summary:
three late exponential phase Rhodococcus sp. RHA1 propane-grown cultures compared to pyruvate-grown cultures
Keywords: growth substrate

overall_design: three two-colour microarrays

first: Jonathon

middle: O

last: Sharp

first: Christopher

middle: M

last: Sales

first: Jie

last: Liu

first: Thomas

middle: K

last: Wood

first: Lindsay

middle: D

last: Eltis

first: William

last: Mohn

first: Lisa

last: Alvarez-Cohen


title: The impact of cell wall alterations on global gene expression.Overexpressor against wild type.

first: Frederique

last: Bitton

summary:
Comparison of DRV1 overexpressor against wild type in stems
Keywords: gene knock in (transgenic)

first: Marie-Laure

last: Martin-Magniette


title: pld-Fonctional analysis of the double mutant phospholipasezeta1,2 in response to abiotic stress

status: Public on Oct 31 2007

summary:
rs06-01_pld - pld - Role of PLDzeta to abiotic stress adaptation - A double mutant PLDzeta1,2 was obtained in a Columbia background. 12-day-old Arabidopsis seedlings, wt or double mutant, were treated with either NaCl (200 mM), mannitol (400 mM) or with 4degreeC temperature during 3 h. 3 biological replicates were pooled.
Keywords: gene knock out,treated vs untreated comparison

overall_design: 3 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Arnould

last: Savoure


title: eqtl analysis (random pair design)-Establishing the network of seed gene expression and analysis of its biodiversity

status: Public on Jun 05 2009

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

summary:
gnp3_tri33-arabidoseed - eqtl analysis (random pair design) - WP3 : Biodiversity of seed traits : state of the art - Comparison of the developping seed transcriptome in 160 Bay0/Sha Recombinant Inbred Lines (RILs) at 10 days after pollinisation.

Keywords: genotype and ecotype comparison

overall_design: 80 dye-swap - CATMA arrays

first: Samira

last: Elftieh

first: Michel

last: Caboche


title: Global variation of copy number in the MCF7 genome

status: Public on Feb 08 2008

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

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

summary:
Identify copy number variation in the MCF7 genome
Keywords: Copy number variation detection

overall_design: MCF7 genomic DNA was hybridized to a 250K Nsp EA mapping array to identify variable copy number regions in the genome.


title: B.thetaiotaomicron wt versus KO2923, NMRI and B6

status: Public on Sep 01 2007

city: Saint Louis

first: Herbert

last: Chiang

department: Center for Genome Sciences

institute: Washington University

summary:
Genome wide transcriptional comparison of B. thetaiotaomicron wild type vs. an isogenic mutant (BT2923::pGERM). Cecal populations of wt or BT2923::pGERM monoassociated 10d with B6 or NMRI gnotobiotic mice fed a standard-chow polysaccharide rich (PR) diet were profiled.
Keywords: wild type versus knockout, in vivo

overall_design: Total RNA was prepared from cecal contents of 10 day monoassociated gnotobiotic mice and hybridized to B. thetaiotaomicron GeneChips.

first: H

first: J

last: Manchester

last: Gordon


title: B.thetaiotaomicron wt versus KO2923, 10% tryptone

summary:
Genome wide transcriptional comparison of B. thetaiotaomicron wild type vs. an isogenic mutant (BT2923::pGERM). Wt or BT2923::pGERM grown in 10% tryptone medium were profiled in duplicate at mid-log and stationary time points.
Keywords: wild type versus knockout, in vitro timepoints

overall_design: Total RNA was prepared from bacteria harvested from growths in 10% tryptone medium and hybridized to B. thetaiotaomicron GeneChips.


title: Desiccation and control transcriptomes of Rhodococcus jostii RHA1

status: Public on May 01 2008

first: Justin

last: LeBlanc

summary:
Here we report the first transcriptomic analysis of a Gram-positive bacterium to desiccation.  Filtered RHA1 cells incubated at either low relative humidity (20%), as an air drying treatment, or high relative humidity (100%), as a control, were transcriptionally profiled over a comprehensive time series.
Keywords: stress response time course

overall_design: Three biological replicates from both the desiccation and control experiments were analyzed using two-colour microarrays.  Over a time series for each experiment, Cy-labelled cDNA from treated and time-zero cells were hybridized, with a dye swap for one of the replicates.

first: Edmilson

middle: R

last: Gonçalves


title: B.thetaiotaomicron wt, TYG (in vitro) and NMRI (in vivo)

summary:
Transcriptional profiles of B. thetaiotaomicron wild type. Bacteria harvested in duplicate from multiple time points during growth in Tryptone-YeastExtract-Glucose (TYG) medium in chemostats were profiled. Cecal populations of wt bacteria monoassociated 10d in NMRI gnotobiotic mice fed a standard-chow polysaccharide rich (PR) diet (n=6 samples) were profiled.
Keywords: in vitro timecourse and in vivo study

overall_design: Total RNA was prepared from harvested bacterium grown in TYG medium and cecal contents of 10 day monoassociated gnotobiotic mice and hybridized to B. thetaiotaomicron GeneChips.


title: BTH-responsive rice genes

status: Public on Jul 30 2007

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

institute: National Institute of Agrobiological Sciences

summary:
Benzothiadiazole (BTH) is a so-called ‘plant activator’ and protects plants from diseases by activating the salicylic-acid (SA) signaling pathway. We identified BTH-responsive genes in rice leaves 24 h after treatment using rice 44K microarray.
Keywords: response to chemical treatment

overall_design: BTH-treated leaves were compared with mock-treated leaves using single-color method with 4 biological replicates.

first: Masaki

last: Shimono

first: Shoji

last: Sugano

first: Akira

last: Nakayama

first: Chang-Jie

last: Jiang


title: nt-kis-CKI role in plant development

status: Public on Aug 09 2007

first: Frederique

last: Bitton

summary:
rs04-08_ntkis - nt-kis - Transcription profiling of NtKIS overexpressing lines - 35S NtKIS (CDK inhibitor) versus Col0
Keywords: gene knock in (transgenic)

overall_design: 2 dye-swap - CATMA arrays

first: Catherine-

last: Bergounioux

first: Marie-Laure

last: Martin-Magniette


title: Genome-wide analysis of early mouse development.

status: Public on Nov 06 2007

city: Stanford

first: Nesanet

last: Mitiku

state: CA

address: 300 Pasteur Drive Alway M313

department: Genetics

institute: Stanford University

summary:
Throughout the course of early development, the reliable occurrence of stereotyped events is imperative. This careful orchestration is dependent upon regulation at the level of gene expression. While all cell types derive from a single fertilized cell and share a single genome, individual cell types differentially utilize this genome. Such differential utilization is essential for the acquisition, maintenance, and modulation of cell properties. In order to better understand the molecular basis of early development, we evaluated the mRNA expression programs of both early post-implantation mouse embryos and differentiating embryonic stem cells using a cDNA microarray platform covering 74% of the mouse genome. Mining of these datasets revealed a strong association across RNA processing, modulation of the cell cycle, and chromatin organization. Genes involved in these processes demonstrated sharp regulation during well-defined biological transitions. Dominant patterns of expression with biologically separable properties were identified. The evolutionary conservation of one cluster in particular suggested a molecular basis for the alignment of the murine and fly developmental programs. Moreover, the data suggest putative gene relationships that may also have broader implications for gene networks connecting the cell cycle to the molecular repertoire of the cell. Design: Dataset is a murine embryonic developmental timecourse consisting of morphologically staged samples from E6.25 to E9.0 (at approximately 0.25d intervals). There two replicates of each sample and there are 13 samples in each biological replicate series. A common reference design was employed.
A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions.
Developmental Stage: morphologically staged samples from E6.25 to E9.0 (at approximately 0.25d intervals)
Keywords: development_or_differentiation_design

overall_design: Using regression correlation


title: A TATA binding protein regulatory network

status: Public on Apr 01 2007

city: Ithaca

first: B. Franklin

last: Pugh

email: fp265@cornell.edu, bfp2@psu.edu

state: NY

address: 465 Biotechnology Bldg.

department: Molecular Biology and Genetics

institute: Cornell University

summary:
Background:  Eukaryotic genes are controlled by proteins that assemble stepwise into a transcription complex.  How the individual biochemically-defined assembly steps are coordinated and applied throughout a genome is largely unknown.  Here, we model and experimentally test a portion of the assembly process involving the regulation of the TATA binding protein (TBP) throughout the yeast genome.  Results:  Biochemical knowledge is used to formulate a series of coupled TBP regulatory reactions involving TFIID, SAGA, NC2, Mot1, and promoter DNA.  The reactions are then linked to basic segments of the transcription cycle and modeled computationally. A single framework is employed, allowing the contribution of specific steps to vary from gene to gene.  Promoter binding and transcriptional output are measured genome-wide using ChIP-chip and expression microarray assays.  Mutagenesis is used to test the framework by shutting down specific parts of the network. Conclusion:  The model accounts for the regulation of TBP at most transcriptionally active promoters and provides a conceptual tool for interpreting genome-wide data sets.  The findings further demonstrate the interconnections of TBP regulation on a genome-wide scale.
Keywords: genetic mutation analysis

overall_design: We analyzed at least 2 dye-swapped individual biological replicates for each mutant.  All included are 16 homotypic (independent biological replicates of reference vs. reference genotype) hybs which were used for the independent "no change" data set.  There are a total of 150 expression arrays.

first: Kathryn

last: Huisinga


title: sdg25 and sdg26-Functional characterization of Arabidopsis NAP1/SET genes

status: Public on Jul 20 2007

first: Soubigou-Taconnat

last: Ludivine

summary:
rs05-12_setii - sdg25 and sdg26 - Differential transcriptome in mutant plants - seeds were sown in vitro and plantlets (Col0 wild type ,and n1, n2, n3, x123, sdg8, vip4,sdg25 and sdg26 mutants)were cultivated during 6 days (1.02 boyes stadge)
Keywords: gene knock out

overall_design: 6 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Wen-hui

middle: h

last: Shen


title: urea-Urea impact on the nitrogen metabolism of plant and on the nitrogen transport systems

status: Public on Oct 16 2007

summary:
ra05-09_urea - urea - What are the transcriptomic plant responses to urea nitrogen supply ? - Columbia Arabidopsis ecotype were grown hydroponically on 0.5 mM NH4NO3 as sole nitrogen source during 35 days under short days. Plants were then placed on 3 nutrient solutions supplemented, either with 1 mM NH4NO3, or with 0.5 mM NH4NO3 + 0.5 mM Urea, or with 1 mM Urea. Root and shoot samples were harvested separately 7 days after these different nitrogen treatments
Keywords: treated vs untreated comparison

overall_design: 8 dye-swap - CATMA arrays

first: Francoise

last: Vedele


title: B.thetaiotaomicron or B. longum mono-association versus B. thetaiotaomicron/B. longum co-colonization, PR chow, NMRI

status: Public on Jan 01 2007

first: Justin

middle: L.

last: Sonnenburg

summary:
Genome wide transcriptional comparison of B. thetaiotaomicron or B. longum mono-association vs. B. thetaiotaomicron bi-association with B. longum.  Cecal populations from 10d colonizations with NMRI gnotobiotic mice fed a standard-chow polysaccharide rich (PR) diet (n=5 samples/group) were profiled.
Keywords: Mono-association vs. Bi-association, in vivo

sample_organism:
Bacteroides thetaiotaomicron
Bifidobacterium longum

overall_design: Total RNA was prepared from cecal contents of 10 day associated gnotobiotic mice and hybridized to B. thetaiotaomicron/B. longum GeneChips.

first: Christina

middle: T

last: Chen

first: Jeffrey

last: Gordon


title: B.thetaiotaomicron mono-association versus B. thetaiotaomicron co-colonization with B. animalis or L. casei, PR chow, B6

summary:
Genome wide transcriptional comparison of B. thetaiotaomicron mono-association vs. B. thetaiotaomicron bi-association with B.animalis or L. casei.  Cecal populations from 20d colonizations with B6 gnotobiotic mice fed a standard-chow polysaccharide rich (PR) diet (n=5 samples/group) were profiled.
Keywords: Mono-association vs. Bi-association, in vivo

overall_design: Total RNA was prepared from cecal contents of 20 day associated gnotobiotic mice and hybridized to B. thetaiotaomicron/B. longum GeneChips.

middle: L


title: B.thetaiotaomicron mono-association versus B. thetaiotaomicron co-colonization with B. longum, PR chow, B6

summary:
Genome wide transcriptional comparison of B. thetaiotaomicron mono-association vs. B. thetaiotaomicron bi-association with B. longum.  Cecal populations from 10d colonizations with b6 gnotobiotic mice fed a standard-chow polysaccharide rich (PR) diet (n=5 samples/group) were profiled.
Keywords: Mono-association vs. Bi-association, in vivo


title: Effects of cholesterol on Rhodococcus sp. RHA1

status: Public on Jan 19 2007

first: Hirofumi

last: Hara

state: BC

address: 2350 Health Science Mall

department: Microbilogy and Immunology

summary:
two cultures one grown on cholesterol and other on pyruvate
Keywords: growth type

overall_design: 3x dual channel slides

first: Robert

middle: V

last: Geize

first: Katherine

last: Yam

first: Thomas

last: Heuser

first: Maarten

last: Wilbrink

first: Matthew

last: Anderton

first: Edith

last: Sim

first: Lubbert

last: Dijkhuizen

first: Julian

middle: E

last: Davies

first: William

last: Mohn

first: Lindsay

last: Eltis


title: Effects of terephthalate on Rhodococcus sp. RHA1

summary:
two cultures one grown on terephthalate and other on pyruvate
Keywords: growth type


title: Effects of phthalate on Rhodococcus sp. RHA1

summary:
two cultures one grown on phthalate and other on pyruvate
Keywords: growth type

first: Willian


title: Soybean cultivars OX951 & OX736, seed coat permeablity comparison

city: London

first: Mark

last: Gijzen

state: ON

address: 1391 Sandford St

department: Agriculture & AgriFood Canada

institute: SCPFRC London

summary:
Soybean cultivars, OX951 & OX736, comparison of seed coat at 3 growth stages, early, mid & late
Keywords: time course

overall_design: 26 microarray slides GPL3015; 2 soybean cultivars, OX951 (with impermeable seed coat) and OX736 (with permeable seed coat); 2 technical reps for each growth stage (dye swap);4 biological reps from 2 consecutive growing seasons, 2004 & 2005 (2 reps per year); 3 growth stages, early (E) 10 to 20 days after pollination (dap), mid (M) 21 to 35 dap and late (L) 36 to 50 dap; total RNA isolated from the whole seed  for the early stage and seed coat only for the mid & late stages. The slide data was analyzed in GeneSpringGX7.3 Agilent Technologies, using background subtracted values. The ratio for OX736/OX951 was calculated from the 2 colour hybridization (same slide) and relative expression for seed coat development as a function of time was calculated using all the slides treated as single channel data.The slide identites are 2004 rep1 GSM97598 to 97603, 2004 rep 2 GSM97606 to 97611, 2005 rep3 GSM97612 to 97617, 2005 rep4 GSM97618 to 97623. Two self test slides were included for 2004 rep1 L stage,  OX951/OX951 and OX736/OX736 , GSM907604-97605

first: Dinah

last: Qutob

first: Pat

last: Moy


title: erwinia-Regulation of the Arabidopsis transcriptome by the type three secretion system (TTSS) of Erwinia amylovora

first: Frederique

last: Bitton

summary:
ra05-02_erwinia - erwinia - Identification of Arabidopsis genes regulataed by Erwinia amylovora and of a subset of Arabiddopsis genes regulated by the type three secretion system of Erwinia amylovora.
Keywords: normal vs disease comparison

first: Marie-Anne

last: Barny

first: Mathilde

last: Fagard

first: Jean-Pierre

middle: P

last: Renou

first: Marie-Laure

last: Martin-Magniette


title: Effects of benzoate on Rhodococcus sp. RHA1

status: Public on Nov 01 2006

first: Michael

last: McLeod

address: 4506 - 2350 Health Sciences Mall

summary:
two cultures one grown on benzoate and other on pyruvate
Keywords: growth type


title: Effects of ethylbenzene on Rhodococcus sp. RHA1

summary:
two cultures one grown on ethylbenzene and other on pyruvate
Keywords: growth type


title: all comparison-Functional characterization of Arabidopsis NAP1/SET genes

first: Soubigou-Taconnat

last: Ludivine

summary:
rs05-12_setii - all comparison - Differential transcriptome in mutant plants - seeds were sown in vitro and plantlets (Col0 wild type ,and n1, n2, n3, x123, sdg8, vip4,sdg25 and sdg26 mutants)were cultivated during 6 days (1.02 boyes stadge)
Keywords: gene knock out

overall_design: 11 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Wen-hui

last: Shen


title: Effects of biphenyl on Rhodococcus sp. RHA1

summary:
two cultures one grown on biphenyl and other on pyruvate
Keywords: growth type


title: RPB1 mutants sensitive to 6-AU

status: Public on Dec 21 2006

city: Aarhus

first: Francisco

last: Malagon

address: C.F. Mollers Alle, Bldg. 130

department: Department of Molecular Biology

country: Denmark

institute: Aarhus University

summary:
Gene expression profiling of RNA pol II mutants. In vivo effects of mutations in residues 260 (rudder), 261 (rudder), 320 (lid), 488 (close to catalytic center), 1230 (required for TFIIS stimulation) and 1103.
Keywords: Gene expression profiling of RNA pol II mutants

overall_design: Gene expression profiling of RPB1 mutants in rich media to characterize the biological response to deficient RNApol II, and to identify genes difficult to transcribe in such mutants.

first: Jeff

last: Strathern


title: Soybean cultivars RCAT-Angora & Harovinton, embryo comparison and development

first: Sangeeta

last: Dhaubhadel

department: Agriculture & Agrifood Canada

type: Genome variation profiling by genome tiling array

summary:
Soybean cultivars RCAT-Angora & Harovinton, comparison of embryos at 30,40,50,60 & 70 days after pollination (dap) and seed development within each cultivar"
Keywords: time course

overall_design: 42 microarray slides GPL3015; 2 soybean cultivars, RCAT-Angora (with high seed isoflavonoid content)& Harovinton (with low seed isoflavonoid content); 2 technical reps for each time point (dye swap); 4 biological reps from 2 locations at London (L) & Delhi (D) Ontario & 2 consecutive growing seasons 2003 and 2004; 5 time points of 30, 40, 50, 60 & 70 dap for D04, L03, L04 and 4 time points of 30, 40, 50 and 70 dap for D03. In addition 2 slides for seed development confirmation D03 30 vs 70 dap RCAT-Angora and 2 for genomic comparison of RCAT-Angora & Harovinton were included. Slide data was analyzed in GeneSpringGX7.3, Agilent technologies, using background subtracted values. The ratio for RCAT/Hvtn was calculated from the 2 colour hybridization (same slide) and the relative expression for embryo development as a function of time (single channel approach) was calculated for each cultivar. The slide identities are L04 GSM94935 - 94944; genomic GSM95945-94946; L03 GSM94947 - 94956; D04 GSM94957 to 94966; D03 GSM94967 - 94976


title: Genes expressed in Arabidopsis pollen: Comparison between Columbia and WS pollen RNAs

status: Public on Sep 22 2006

summary:
RNAs of Pollen from Columbia and WS were compared
Keywords: ecotype comparison

overall_design: 1 dye-swap - CATMA arrays


title: sva53 mutant ovary

status: Public on Sep 20 2006

first: Shuji

last: Shigenobu

summary:
Gene expression profiles between sva53 mutant and control ovaries (sva53/+) were examined.
Keywords: mutant assay

overall_design: Total RNA was purified from the ovaries of ~7-day-old sva53 mutant flies. Two pairs of ovaries were pooled for each of the 3 independent experiments. sva53/+ flies serve as a control. Total RNA purified from three pairs of control ovaries were used as a common reference in all hybridizations.

first: Masanori

last: Mukai

first: Kayo

last: Arita

first: Yoshiki

last: Hayashi

first: Yu

last: Kitadate

first: Satoru

last: Kobayashi


title: B.thetaiotaomicron wt versus KO3172, PR chow, NMRI

status: Public on May 14 2006

first: Justin

last: Sonnenburg

summary:
Genome wide trascriptional comparison of B. thetaiotaomicron wild-type vs. an isogenic mutant  (BT3172::pGERM).  Cecal populations of wt or BT3172::pGERM monoassociated 10d with NMRI gnotobiotic mice fed a standard-chow polysaccharide rich (PR) diet (n=5 samples/group) were profiled.
Keywords: Wild-type versus Knockout, in vivo

overall_design: Total RNA was prepared from cecal contents of 10 day monoassociated gnotobiotic mice and hybridized to B. thetaiotaomicron GeneChips.

first: Erica

first: Jill

last: Manchester

first: Elizabeth

last: Hansen

first: Herber

middle: C

last: Chiang

first: Jeffrey

middle: I

last: Gordon


title: B. thetaiotaomicron before and after lactose addition to tryptone media 2

status: Public on Sep 01 2006

city: St. Louis

first: Magnus

last: Bjursell

address: 4444 Forest Park Ave

institute: Washington University School of Medicine

summary:
B. thetaiotaomicron was grown in a batch culture fermenter containing tryptone media. Lactose (final concentration 0.2%) was added at OD600 = 0.3. Samples were taken immediately before and 60 minutes after addition.
Keywords: time course

first: Eric

last: Martens


title: B. thetaiotaomicron before and after galactose addition to tryptone media

summary:
B. thetaiotaomicron was grown in a batch culture fermenter containing tryptone media. Galactose (final concentration 0.2%) was added at OD600 = 0.3. Samples were taken immediately before and 60 minutes after addition.
Keywords: time course


title: Gene expression in Drosophila treated with P. nigrum, pyrethrin or P. nigrum plus pyrethrin

status: Public on Mar 31 2006

city: Ottawa

first: Helen

middle: Rose

last: Jensen

state: Ontario

address: 30 Marie-Curie street

department: Ottawa-Carleton Institute of Biology

institute: University of Ottawa

summary:
The purpose of this experiment was to assess the effect of a synergistic combination of natural pyrethrin and an ethylacetate extract of Piper nigrum seeds (a botanical insecticide).  This effect was compared to the effects of P. nigrum or pyrethrin used alone.  Due to the synergistic nature of the mixture, it was predicted that gene expression profiles in this treatment would reflect this effect.
Keywords: insecticide response, stress-response

overall_design: Three sets of comparisons were performed.  Drosophila exposed to either P. nigrum, pyrethrin or pyrethrin plus P. nigrum were compared to Drosophila exposed to the carrier solvent ethanol.  These three data sets were then compared.

first: Ian

last: Scott

first: Vance

last: Trudeau

first: Steve

last: Sims

first: John Thor

last: Arnason


title: Soybean cultivars,Soybean Hydrophobic Protein(HPS) comparison

status: Public on Mar 21 2006

first: Mark

last: Gijzen

summary:
The Hydrophobic protein from soybean (HPS) locus is polymorphic among soybean cultivars and copy-number changes in the tandem array at this locus are directly correlated with expression level and seed coat luster phenotypes.
Keywords: comparative genomic hybridization

overall_design:
The indentity for HPS on the array is AW156395, Gm-r1070-2255. ExptI Mukden(shiny) vs OX281(dull) biological rep 1;ExptII Mukden vs OX281 biological rep 2;ExptIII Harosoy 63(dull) vs Sooty(bloom) biological rep 1
6 slide hybridizations including dye swap,6 genomic DNA samples,4 soybean cultivars

first: Kuflom

last: Kuflu

first: Pat

last: Moy


title: B. thetaiotaomicron harvested from cecum of P17 and P30 NMRI mice

summary:
Gnotobiotic NMRI mice were colonized at birth with B. thetaiotaomicron. Mice were sacrificed at P17 or P30, cecal contents were harvested and used for transcriptional profiling.
Keywords: developmental timepoints, in vivo


title: Evalutation of the effect of ethanol upon gene expression in adult Drosophila melanogaster

summary:
This experiment was intended to determine if topical exposure to ethanol led to significant changes in gene expression in adult Drosophila melanogaster.   It was determined that topical exposure to ethanol did not lead to a strong differential expression of genes in Drosophila after 4 hours.
Keywords: Ethanol response, stress response

overall_design: The effect of topical treatment with 99% ethanol was compared to the effect of a water treatment which was used as a control and the differential expression between these two treatments was assessed four hours after treatment. Two biological replicates of each treatment were compared for a total of two microarray hybridizations


title: B. thetaiotaomicron before and after lactose addition to tryptone media 1

overall_design: B. thetaiotaomicron was grown in a batch culture fermenter containing tryptone media. Lactose (final concentration 0.2%) was added at OD600 = 0.3. Samples were taken immediately before and 60 minutes after addition.


title: Like-like hybridization to test 7K3 platform variability

summary:
This experiment compared separate pools of Drosophila which received identical topical treatments of 99% ethanol 6 hours after exposure.  The purpose of this was to assess the degree of natural variability that could be expected to be observed between samples in the absence of distince treatments.  This was to allow for greater confidence in interpreting the results of other experiments which compared insects that received different treatments.  It was found that a differential expression log2ratio range  of -1.41 to 1.41 encompassed over 99% of all genes in this experiment.
Keywords: platform background variation evaluation

overall_design: 8 microarray chips were hybridized with RNA extracted from Drosophila treated with ethanol.  There were four biological replicates and four dye-reversal replicates.


title: High Resolution Copy Number Analysis of Paraffin Embedded Archival Tissue Using SNP BeadArrays

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

summary:
High density SNP microarrays provide insight into the genomic events that occur in diseases like cancer by their capability to measure both LOH and genomic copy numbers. Where currently available methods are restricted to the use of fresh frozen tissue, we now describe the design and validation of copy number measurements using the Illumina BeadArray platform and its
application to formalin fixed, paraffin embedded (FFPE) tissue. In fresh frozen tissue, using a set of colorectal tumors with numerous chromosomal
aberrations, our method measures copy number patterns that are comparable to values from established platforms, like Affymetrix GeneChip and BAC array-CGH. Moreover, paired comparisons of fresh frozen and FFPE tissue showed nearly identical patterns of genomic changes. We conclude that this method enables the use of paraffin embedded material for research into both LOH and numerical chromosomal abnormalities. These findings make the large pathological archives available for genomic analysis, which could be especially relevant for hereditary disease where fresh material from affected relatives is rarely available.
Keywords: platform comparison and method development

overall_design:
Colorectal tumor tissue and corresponding normal tissue from 4 patients was
used. The samples included a rectal adenoma (T514), one right-sided Dukes B (T44) and two Dukes C carcinomas (T106, T108).
Copy number and genotyping was compared between the following platforms:
- Illumina Sentrix BeadArrays with linkage mapping panel version IV
- Affymetrix GeneChip Mapping 10K Xba1 arrays
- 3.7 K LUMC BAC array
The first Illumina experiment (201 suffixes) showed low intensity values, and was repeated (260 suffixes) The Sentrix plates were filled up with other patient material to process a total of 24 samples with different types of normal and affected tissue.
Normal samples have been used for normalization

first: Tom

last: van Wezel

first: Esther

middle: H

last: Lips

first: Ronald

last: van Eijk

first: Paul

last: Eilers

first: K�roly

last: Szuhai

first: Cisca

last: Wijmenga

first: Hans

last: Morreau


status: Public on Jan 25 2006

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

type:
Expression profiling by array
Genome variation profiling by array

summary:
Data underlying Sander et al., Oncogene 2005, June 20, Comparative genomic hybridization on mouse cDNA microarrays and its application to a murine lymphoma model.  Includes both array CGH and expression data.
Abstract: Microarray-based formats offer a high-resolution alternative to conventional, chromosome-based comparative genomic hybridization (CGH) methods for assessing DNA copy number alteration (CNA) genome-wide in human cancer. For murine tumors, array CGH should provide even greater advantage, since murine chromosomes are more difficult to individually discern. We report here the adaptation and evaluation of a cDNA microarray-based CGH method for the routine characterization of CNAs in murine tumors, using mouse cDNA microarrays representing approximately 14,000 different genes, thereby providing an average mapping resolution of 109 kb. As a first application, we have characterized CNAs in a set of 10 primary and recurrent lymphomas derived from a Myc-induced murine lymphoma model. In primary lymphomas and more commonly in Myc-independent relapses, we identified a recurrent genomic DNA loss at chromosome 3G3-3H4, and recurrent amplifications at chromosome 3F2.1-3G3 and chromosome 15E1/E2-15F3, the boundaries of which we defined with high resolution. Further, by profiling gene expression using the same microarray platform, we identified within CNAs the relevant subset of candidate cancer genes displaying comparably altered expression, including Mcl1 (myeloid cell leukemia sequence 1), a highly expressed antiapoptotic gene residing within the chr 3 amplicon peak. CGH on mouse cDNA microarrays therefore represents a reliable method for the high-resolution characterization of CNAs in murine tumors, and a powerful approach for elucidating the molecular events in tumor development and progression in murine models.
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, arrayCGH, expression profiling

overall_design: Using regression correlation

first: Lars

last: Bullinger


title: Drosophila gene expression in response to the botanical insecticide Piper nigrum

status: Public on Jan 24 2006

first: Helen

last: Jensen

summary:
This experiment was used to determine the effect of a botanical insecticide upon gene expression profiles in Drosophila melanogaster.  Adult female Drosophila (oregon-R strain) were treated with an ethylacetate extract of Piper nigrum (Piperaceae) seeds formulated in 99% ethanol.  Treatment was topical, using a Potter's tower to administer a total of 2 mL of a 0.9mg/mL concentration.  Control treatment was identical except flies were treated with 99% ethanol as a solvent control.  Gene expression was studied four hours post-treatment.
Keywords: insecticide response, stress-response

overall_design: The design is a direct comparison between total RNA of treated and untreated insects.  Sample size is two and two reverse label hybridizations were done.  Each sample is a pool of 240 insects which received the same treatment simultaneously.

last: Scott

first: Steven

first: John


title: ALL Translocations

status: Public on Dec 21 2005

summary:
Cell lines and pediatric acute lymphoblastic leukemia samples with either BCR/ABL, TEL/AML1 or MLL abnormalities
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Bernard

last: Fine


title: Effects of methotrexate on S3 Drosophila cells and Drosophila ovaries

status: Public on Oct 22 2005

city: Kingston

first: Joslynn

middle: Gayle

last: Affleck

address: 116 Barrie St.

department: Biology

institute: Queen's University

summary:
Comparison of transcript abundance between control (untreated) and methotrexate treated S3 Drosophila cells and ovaries disected from female flies.
Keywords: Stress response

overall_design: S3 cells were exposed to 0 or 5.2 X 10^-8 M MTX for 4 days then harvested.  Flies were exposed to 0 or 5 ppm MTX for 5 days then ovaries were dissected.  RNA was extracted from S3 cells and ovaries.  4 S3 microarrays with one dye-swap and 2 ovary microarrays swapping dyes were hybridized to spotted cDNA microarrays.

middle: G

first: Katerina

last: Neumann

first: Lily

last: Wong

first: Virginia

last: Walker


title: In vitro and in vivo transcriptional profiling of Bacteroides thetaiotaomicron

status: Public on Mar 30 2005

first: Justin

last: Sonnenburg

address: 4444 Forest Park

summary:
Transcriptional profiling of Bacteroides thetaiotaomicron was performed on samples taken from (i) chemostat cultures (in vitro) and (ii) from the ceca of gnotobiotic monoassociated NMRI mice (in vivo).  In vitro profiles were obtained from biological duplicate cultures taken at five timepoints from log to stationary phase in three types of media: (i) minimal media glucose (MM-G), (ii) minimal media maltotriose (MM-M), and (iii) rich media (TYG).  In vivo profiling was performed on 12 mice, each colonized with B. thetaiotaomicron for ten days.  The in vivo profiling was conducted in two separate experiments: (i) 6 male NMRI mice fed standard polysaccharide rich mouse chow and (ii) 3 male NMRI mice fed standard polysaccharide rich mouse chow and 3 male NMRI mice fed a simple sugar diet containing glucose and sucrose but deficient in polysaccharides.
Keywords: other

first: Jian

last: Xu

first: Douglas

last: Leip

first: Chien-Huan

last: Chen

first: Benjamin

last: Westover

first: Jeremy

last: Weatherford

last: Buhler

first: Jeffrey

last: Gordon


title: Estrogen-responsive genes in the parenchyma and fat pad of the bovine mammary gland by microarray analysis

status: Public on Jan 28 2006

city: Beltsville

first: Robert

middle: W

last: Li

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

summary:
Characterizing estrogen-responsive genes is an essential step towards fully understanding mechanisms of estrogen action during mammary gland development and function. To catalogue these genes, sixteen prepubertal heifers were used in a 2 x 2 factorial with ovarian status (intact or ovariectomized) as the first factor and estrogen treatment as the second (control or estradiol). Heifers were ovariectomized at approximately 4.5 months of age and estrogen treatments were initiated one month later. After 3 days of treatment, gene expression in the parenchyma and fat pad of the bovine mammary gland was analyzed using a high-density oligonucleotide microarray.  This microarray contained probes representing 40,808 Tentative Consensus sequences from the TIGR Bos taurus Gene Index and 4,575 singletons derived from libraries of pooled mammary gland and gut tissues. Microarray data were analyzed using the SAS Mixed Procedure with permutation testing. A total of 125 estrogen-responsive genes were identified using an experiment-wide permutation-based significance level of P < 0.1. Among these genes are known estrogen-targeted genes such as stanniocalcin 1, alpha-1-antiproteinase, progesterone receptor, nucleobindin 2, insulin-like growth factor 1, and tissue factor pathway inhibitor. However, the majority of the genes identified were not previously reported to be estrogen-responsive. In silico mapping and an estrogen response element (ERE) search indicated potential EREs in the promoter regions of some of these novel estrogen-responsive genes. The distinctive expression patterns regulated by estrogen in parenchyma and fat pad suggest mechanisms of action and reciprocal signaling between cell types.
Keywords: Cell type comparision, two class unpaired design

overall_design: Sixteen prepubertal heifers were used in a 2 x 2 factorial with ovarian status (intact or ovariectomized) as the first factor and estrogen treatment as the second (control or estradiol). Two tissues (parenchyma and fat pad) from each heifer were sampled. 32 single-channel microarray hybridization were performed.

first: Mathhew

middle: J

last: Meyer

first: Curt

last: Van Tassell

first: Tad

middle: S

last: Sonstegard

first: Erin

last: Connor

first: Michael

last: Van Amburgh

first: Yves

last: Boisclair

first: Anthony

last: Capuco