title: Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development

first: Wen

address: 1675 Observatory Dr. Room 634

department: Department of Dairy Science

institute: University of Wisconsin - Madison

summary: Using microarrays, genome-wide RNA expression was profiled and compared for in vitro fertilization (IVF) - derived blastocysts and embryos undergoing degenerative development up to the same time point. Surprisingly similar transcriptomic profiles were found in degenerative embryos and blastocysts. Nonetheless, we identified 67 transcripts that significantly differed between these two groups of embryos at a 15% false discovery rate, including 33 transcripts showing at least a two-fold difference. Several signaling and metabolic pathways were found to be associated with the developmental status of embryos, among which were previously known important steroid biosynthesis and cell communication pathways in early embryonic development.

overall_design: Three biological replicates for each of blastocysts and degenerative embryos.

last: Yandell

first: Hasan

last: Khatib


title: Murine Flt3L-derived dendritic cell-mediated early immune responses are critical to controlling cell-free HTLV-1 infection

status: Public on Oct 28 2010

city: Doylestown

first: Saifur

last: Rahman

state: PA

address: 3805 Old Easton Rd

department: Microbiology and Immunology

country: USA

institute: Drexel University

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

overall_design: Refer to individual Series


title: Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes

status: Public on Oct 19 2010

city: Philadelphia

first: Daniel

middle: Francis

last: Simola

address: 1041 BRB II/III

department: Cell and Developmental Biology

institute: University of Pennsylvania

sample_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus


title: To identify novel metastasis-associated gene candidates in colorectal cancer

status: Public on Oct 16 2010

city: Taipei

first: Yi-Shing

last: Lin

address: NanGang

country: Taiwan

institute: Welgene Biotech.co., Ltd

summary: A gene expression profiling suggested some gene candidates associated with colorectal cancer (CRC) metastasis, which were validated by qPCR investigation of the mRNA levels in clinical specimens

overall_design: Two-condition experiment,  tumor tissue versus the adjacent non-tumor tissue. Biological replicates: 4

first: Chun-Chung

last: Lee

first: Wei-Shone

last: Chen

first: Chia-Chi

first: Tze-Sing

last: Huang


title: Cellular transcription profile of differentiated NTNeurons infected with herpes simplex virus 1

city: Bethesda

first: Falko

last: Schmeisser

state: MD

address: 8800 Rockville Pike, building 29A, room 3C-05

department: DVP

institute: FDA/CBER

summary:
Differentiated NT2 cells are a potentially useful model system to study herpes simples virus (HSV) replication in human neurons.  These cells can be irreversibly differentiated into NT-neurons in the presence of retinoic acid and non-dividing cultures NT-neurons can be maintained for up to several months without retinoic acid.  HSV is capable of infecting and replicating in differentiated NT-neurons and thus differentiated NT-neurons provide a ready source of human post-mitotic cells which can be useful to study certain aspects of the interaction of HSV and the neuron.  Microarray analysis was used to examine how HSV-1 infection modulates cellular transcription in human NT-neurons, focusing on changes that take place during the first 24 hours following infection and compared to changes resulting from infection with inactivated virus.  In addition, the transcriptional changes resulting from virus infection of neurons were compared to those observed in primary human fibroblasts.  At early times after HSV infection a small number of cellular transcripts in NT-Neurons appear to be increased in abundance.  Most of these transcripts that are up-regulated after infection are not unique to neuronal cells, and possibly represent a common cellular response to HSV infection.  A few transcripts were not detected in infected human fibroblasts and may represent part of a transcriptional profile specific to this type of human neuronal cell.  In contrast to the situation at early times after infection, analysis of cellular transcripts in NT-neurons at late times after infection is complicated by the overall profound decrease in cellular transcription.  Thus, microarray analysis appeared to be most useful as a screening method for transcription changes following infection at early times after virus infection of NT-neurons.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series.
Two-condition experiments, HSV-1 (active or inactivated virus) infected versus uninfected cells (NTNeurons or Detroit 551 fibroblasts), 3 or 4 independent biological replicate sets per sub-series (uninfected/infected) in dual channel array setup (Cy3/Cy5).


title: Validation data for Lawrence Livermore Microbial Detection Arrays

status: Public on Oct 15 2010

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

sample_organism: Human respiratory syncytial virus A strain Long


title: Modulation of the transcriptional response to recombinant IFN-β by Acetaminophen

status: Public on Oct 18 2010

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

summary:
We examined the effect of acetaminophen (APAP) on the transcriptional response induced by interferon-β (IFN-β). Transcript levels from total RNA isolated rom murine livers were determined using G4121B whole genome arrays.

Keywords: Pharmakinetics, drug treatment

overall_design: 6-8 week male CD-1 mice were administered vehicle alone, APAP, IFN-β or IFN-β + APAP (n=5 per treatment per time point 40 animals total) and were euthanized at 1.5 or 4 hours post-treatment. Agilent 22k whole genome arrays were used to measure changes in mRNA transcripts in the liver mRNA. Stratatagene Universal Mouse RNA was used as a reference.

first: Aaron

last: Farnsworth

first: Ana

middle: S

last: Flaman

first: Shiv

last: Prasad

first: Caroline

last: Gravel

first: Carole

middle: L

last: Yauk

first: Xugang

last: Li


title: Adult_mouse_testis_CREM_ChIP_chip

status: Public on Oct 13 2010

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

type: Genome binding/occupancy profiling by array

summary: Germ cells from adult mouse testes were isolated and ChIPed by CREM antibody. The purpose is to identify potential CREM targets during spermatogenesis.

overall_design: The CREM antibody ChIPed DNA segments were labeled with Cy5 and goat IgG ChIPed segments were labeled with Cy3 as control. No duplicates were designed.

first: Yujian

last: Wu

first: Xiwen

first: Min

last: Wang

first: Chunsheng

last: Han


title: Time series of Balb/c spleen infected with Plasmodium yoelii non-lethal vs lethal strains

status: Public on Oct 12 2010

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

country: Spain

institute: IDIBAPS

summary: Knowledge on the dynamic features of the processes driven by malaria parasites in the spleen, our biggest lymphoid organ, is lacking. We have implemented intravital microscopy and magnetic resonance imaging of the mouse spleen in experimental infections with the Plasmodium yoelii non-lethal (17X) and lethal (17XL) strains. Notably, there was higher parasite accumulation, reduced motility, lost of directionality and different T2 relaxation times only in spleens of mice infected with the 17X strain. Moreover, these differences were associated with the formation of a strain-specific induced spleen tissue barrier, with macrophage-clearance escape, and with cytoadherence of infected reticulocytes to this barrier. This is a novel spleen-immune evasion mechanism in which parasite-induced spleen remodeling and adherence to this organ allow establishment of chronic infections.

overall_design: We performed time-series global transcriptional analyses from spleens of mice infected with the P. yoelii 17X and 17XL strains at days 3, 4, 5, 10% and 50% of parasitemia  post-infection, together with  non-infected spleens as a reference day 0, using commercially available arrays representing the complete mouse genome (Agilent Whole Mouse Genome G4122A).

first: Anna

last: Rosanas-Urgell

first: Hernando

middle: A

last: del Portillo


title: Gene expression analysis of diet induced obesity model zebrafish

city: Tsu

first: oka

last: takehiko

state: Mie

address: 2-174 Edobashi

department: Graduate School of Medicine

country: Japan

institute: mie university

summary: As microarray based gene expression profiling is well suited to study the complex diseases such as obesity, we revealed gene expression changes of fat tissues on obesity model zebrafish to elcidate the pathophysiological function of each fat tissue in metabolic syndrome.

overall_design: Zebrafish in over-feeding group were fed three times per day with Artemia (60 mg cysts/fish/day) through 8weeks. 1week over-feeding group were fed three times per day with Artemia (60 mg cysts/fish/day) through 1week. For caloric restriction, zebrafish were fed with Artemia (2.5 mg cysts/fish/day) for 2 weeks after over-fed with Artemia for 8 weeks.

first: Takehiko

last: Oka

first: Yuhei

last: Nishimura

first: Toshio

last: Tanaka


title: S. coelicolor LY2517 R5- medium time course study

status: Public on Oct 25 2010

city: Minneapolis

first: Marlene

last: Castro-Melchor

state: MN

address: 421 Washington Ave SE

department: Department of Chemical Engineering and Materials Science

institute: University of Minnesota

first: Wei-Shou

last: Hu


title: Gene expression changes in the female zebrafish (Danio rerio) brain in response to acute exposure to methylmercury

status: Public on Oct 01 2010

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Methylmercury (MeHg) is a potent neurotoxin and endocrine disruptor that accumulates in aquatic systems. Previous studies have shown suppression of hormone levels in both male and female fish, suggesting effects on gonadotropin regulation in the brain. We investigated the gene expression profile in adult female zebrafish whole brain induced by acute (96 hr) MeHg exposure. Fish were exposed by injection to 0 or 0.5 µg MeHg/g. Gene expression changes in the brain were examined using a two-color 22,000 feature zebrafish microarray. At a significance level of p<0.01, 79 genes were up-regulated and 76 genes were down-regulated in response to MeHg exposure. Individual genes exhibiting altered expression in response to MeHg exposure implicate effects on glutathione metabolism and GABA-A receptors in the mechanism of MeHg neurotoxicity. Gene ontology (GO) terms significantly enriched among altered genes included protein folding, cell redox homeostasis, and steroid biosynthetic process. The most affected biological functions were related to the nervous system development and function, as well as lipid metabolism and molecular transport. These results support the involvement of oxidative stress and effects on protein structure in the mechanism of action of MeHg in the female brain. Future studies will compare the gene expression profile induced in response to MeHg with that induced by other toxins and investigate responsive genes as potential biomarkers of MeHg exposure.

overall_design:
Wild-type strain AB-1 zebrafish (Zebrafish International Resource Center, University of Oregon, Eugene, OR) were cultured at the Columbia Environmental Research Center (CERC), USGS, for MeHg exposures. Adult female zebrafish were injected with 0 μg/g or 0.5 μg/g MeHg in 2 µL Na2CO3 (pH 6.98)/g body weight.  After 96 hr, fish were anesthetized using ethyl 3-aminobenzoate methanesulfonate (MS-222, Sigma, St. Louis, MO). Whole brains were removed, flash frozen with liquid nitrogen and stored at 80°C.

For the microarray experiment, two zebrafish brains were pooled per sample. Four pooled samples were taken from fish treated with 0.5 μg/g of MeHg, and the other five were taken from control fish treated with sodium carbonate. Array hybridizations were performed using a reference design, where each sample was compared to a reference sample. The reference sample consisted of equal amounts of RNA from control and treated female brains. Five replicates for the control and four replicates for the treated were analyzed. cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer’s kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit and Agilent 60-mer oligo microarray processing protocol; Agilent, Palo Alto, CA).

first: Richter

last: Catherine

first: Garcia-Reyero

last: Natalia

first: Martyniuk

last: Chris

first: Knoebl

last: Iris

first: Pope

last: Marie

first: Wright-Osment

last: Maureen

first: Denslow

middle: D

last: Nancy

first: Tillitt

middle: E

last: Donald


title: Gene Expression Profiles of RAW264.7 Macrophages Stimulated with Two Commonly Used Preparations of LPS

city: Denver

first: Ivana

middle: V

last: Yang

state: CO

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

summary:
Background:  Toll-like family of receptors recognizes pathogen-associated molecular patterns (PAMPs) from different organisms.  TLR4 is the receptor for bacterial lipopolysaccharide (LPS), dsRNA viral mimic poly(I:C) binds to TLR3, and bacterial CpG DNA signals through TLR9.  TLR4 signaling is mediated by adaptor molecules Myd88 and TRIF while TLR3 pathway involves only the TRIF adaptor and TLR9 signals solely through Myd88.      Methods:  To identify genes other than those in TLR pathways that mediate macrophage response to different PAMPs, RAW264.7 cells were stimulated with LPS, poly(I:C), or CpG DNA, and RNA was profiled on microarrays 6 hrs and 24 hrs post-treatment.  Gene expression data were analyzed to determine genes, pathways and transcriptional networks that are in common and unique to each of the three TLR stimuli.  Potentially novel candidates revealed by this analysis were tested for their role in innate immunity using RNA interference.    Results:  Many genes are differentially regulated by LPS and poly(I:C) at both 6 hrs and 24 hrs following treatment, while CpG DNA elicits a much less pronounced transcriptional response.  By analyzing gene expression data for networks and pathways, we prioritized differentially expressed genes that are in common to all three PAMPs as well as those shared by LPS and poly(I:C).  Knockdown by RNA interference of two genes, Plec1 and TPST1, inhibited production of IL-6 in response to LPS in cultured macrophages.      Conclusions:  We have identified novel innate immunity genes that may be important in macrophage response to LPS, poly(I:C), and CpG DNA stimuli.  Our results provide potential biomarkers and therapeutic targets that should be further investigated in mice and human populations.

Keywords: time course

overall_design: For each treatment (Sigma LPS, LIST LPS, and media only), three biological replicates (separate macrophage cultures and RNA isolations) were profiled.  Each sample was labeled with Cy3 and Cy5 and co-hybridized with Stratagene Universal Mouse Reference (dye flip techical replicates).  Expression at 2 timepoints (6 and 24 hours post-treatment) was assessed.

first: Wayne

last: Jiang

first: David

last: Pisetsky

last: Schwartz

first: Holly

middle: R

last: Rutledge


title: Comparison of bovine undifferentiated MSCs, chondrogenic MSCs and chondrocytes in 3D culture

status: Public on Oct 02 2010

first: Alice

middle: H

last: Huang

address: 424 Stemmler Hall, 3450 Hamilton Walk

department: Bioengineering

summary: Bovine chondrocyte-seeded and mesenchymal stem cell (MSC)-seeded agarose were cultured for 28 days in chemically defined media containing 10 ng/mL TGF-beta3.  Chondrogenic differentiated MSCs were compared to chondrocytes at this timepoint and to undifferentiated MSCs harvested at day 0.

overall_design: Donor-matched sets of chondrocytes and MSCs were used, with three donors total.

first: Ashley

last: Stein

first: Robert

last: Mauck


title: QX recombinant inbred advanced intercross lines of C. elegans

city: New York

first: Matthew

last: Rockman

state: NY

address: 100 Washington Sq. E.

institute: New York University

summary: Mutation generates the heritable variation that genetic drift and natural selection shape. In classical quantitative genetic models, drift is a function of the effective population size and acts uniformly across traits, while mutation and selection act trait-specifically. We identified thousands of quantitative trait loci (QTL) influencing transcript abundance traits in a cross of two C. elegans strains; although trait-specific mutation and selection explained some of the observed pattern of QTL distribution, the pattern was better explained by trait-independent variation in the intensity of selection on linked sites. Our results suggest that traits in C. elegans exhibit different levels of variation less because of their own attributes than because of differences in the effective population sizes of the genomic regions harboring their underlying loci.

overall_design: RNA was measured from developmentally synchronized young adult hermaprhodites from each of 208 recombinant inbred advanced intercross lines. Strains were grown at 20 degrees C on NGM plates seeded with OP50 E. coli, following standard C. elegans procedures. Experimental methods follow those described in Capra et al., PLoS ONE 3, e4055 (2008). The genotypes of the 208 strains are detailed in Rockman and Kruglyak, PLoS Genet 5, e1000419 (2009). Each sample was cohybridized with a common pooled reference, with Cy3 and Cy5 assigned randomly to sample or reference for each experiment. Please also see 'Genotypes.txt' file available on the Series record for strain/genotype details.

first: Sonja

last: Skrovanek

first: Leonid

last: Kruglyak


title: The suitability of statistical tests according to characteristics in variation of expression microarray data

status: Public on Nov 17 2010

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

type:
Third-party reanalysis
Expression profiling by array

summary:
Microarray technology has enabled the measurement of comprehensive transcriptomic information. However, each data entry may reflect trivial individual differences among samples and also contain technical noise. Therefore, the certainty of each observed difference should be confirmed at earlier steps of the analyses, and statistical tests are frequently used for this purpose. Since a microarray measures a huge number of genes and the results are processed simultaneously, concerns regarding problems of multiplicity have been raised to the tests. To deal with these problems, several methodologies have been proposed, making the tests very conservative. Indeed, arbitrary tuning of the test threshold has also been introduced to relax the test conditions. However, the appropriateness of the multiplicity problems as well as the compensation methods has not been confirmed.

The appropriateness of the compensation methods was checked by means of coincidence of the premises of the methodologies with the observed characteristics found in real data of two typical platforms of microarray analysis. Normality was observed in within-group data variations, supporting applications of parametric tests. However, genes displayed their own tendencies in the magnitude of variations, and the distributions of P-values were rather complex and varied; these characteristics are inconsistent with the premises of the compensation methodologies. Additionally, the appropriateness of the proposed multiplicities is reconsidered. When we observed differences in the transcriptome, the family-wise error rate should not be considered, since analyses at higher levels would not be influenced by a few false positives among the huge numbers of true information. Likely, concerns for a false discovery rate are not suitable for the point null hypotheses on expression levels, since the rate of true null hypotheses should be rare in contradiction to the premise of the methodology.

Although compensation methods have been recommended to deal with the problem of multiplicity, the compensations are actually inappropriate for many of the applications of transcriptome analyses. Compensations are not only unnecessary, but will increase the occurrence of false negative errors, and arbitrary adjustment of the threshold damages the objectivity of the tests. Rather, the results of parametric tests should be evaluated directly.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Leukocyte accumulation in graft blood vessels during self-limiting acute rejection of rat kidneys Immunobiology

status: Public on Sep 24 2010

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

country: Germany

institute: Uniklinikum Giessen

summary: Acute rejection episodes trigger chronic renal allograft vasculopathy. Numerous leukocytes, predominantly monocytes, accumulate in graft blood vessels during reversible acute rejection preceding chronic rejection of rat kidneys. We speculate that they contribute to transplant vasculopathy and set out to characterize them. Allogeneic renal transplantation was performed in the Fischer 344 to Lewis rat strain combination, Lewis isografts served as controls. Leukocytes were harvested by intensive perfusion of graft blood vessels and subjected to flow cytometry, quantitative RT-PCR and genome-wide transcriptional profiling.

overall_design: Kidneys of LEW and F344 rats were transplanted in LEW rats. Five biological replicates were performed for both isogenic and allogenic transplantation. Transcriptomes of allogenics were compared to isogenics on 5 dual-color hybridizations.

first: Anna

last: Zakrzewicz

first: Veronika

last: Grau


title: Heterogeneity of Breast Cancer Vasculature

status: Public on Sep 19 2010

city: Montreal

first: Francois

last: Pepin

state: Quebec

address: 1160 Pine Av W

institute: McGill University

summary: Tumor-associated breast vasculature was laser-cappture microdissected from IDC breast cancer cases. The goal of the study was to characterize the heterogeneity of breast tumor-associated vasculature and identify gene expression signatures predictive of clinical outcome.

overall_design: common reference design, 32 samples

first: Julie

last: Laferriere

first: Svetlana

last: Sadekova

first: Margarita

last: Souleimanova

first: Hong

last: Zhao

first: Greg

last: Finak

first: Nicholas

last: Bertos

first: Michael

last: Hallett

first: Morag

last: Park


title: Microarray analysis of V. cholerae genes differentially expressed in rabbit ileal loop fluid and mucus

status: Public on Sep 29 2010

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

first: Nadia

last: Dolganov


title: Molecular profiling of cytomegalovirus-induced human CD8+ T cell differentiation

status: Public on Sep 16 2010

city: Amsterdam

first: Perry

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

summary: CD8+ T cells play a critical role in the immune response to viral pathogens. Persistent human CMV (HCMV)  infection results in a strong increase in the number of virus-specific, quiescent effector-type CD8+ T cells  with constitutive cytolytic activity, but the molecular pathways involved in the induction and maintenance of  these cells are unknown. We show here that HCMV infection induced acute and lasting changes in the transcriptomes  of virus-reactive T cells collected from HCMV-seropositive patients at distinct stages of infection.  Enhanced cell cycle and metabolic activity was restricted to the acute phase of the response, but at all stages,  HCMV-specific CD8+ T cells expressed the Th1-associated transcription factors T-bet (TBX21) and eomesodermin  (EOMES), in parallel with continuous expression of IFNG mRNA and IFN-g–regulated genes. The cytolytic  proteins granzyme B and perforin as well as the fractalkine-binding chemokine receptor CX3CR1 were found  in virus-reactive cells throughout the response. During HCMV latency, virus-specific CD8+ T cells lacked the  typical features of exhausted cells found in other chronic infections. Persistent effector cell traits together with  the permanent changes in chemokine receptor usage of virus-specific, nonexhausted, long-lived CD8+ T cells  may be crucial to maintain lifelong protection from HCMV reactivation.

overall_design: CD8+ T cells of naive, effector, and memory type were isolated from six latently chronic-infected healthy donors. For RNA isolation and microarray analysis, 3 independent donors  and a pool of 3 additional healthy individuals were used. Total RNA of all naive CD8+ T cells was pooled and used as a common reference sample.

first: Kirsten

middle: M

last: Hertoghs

first: Rene

last: van Lier


title: S. coelicolor M145 SMM medium time course study

first: Marlene

last: Castro-Melchor


title: Root transcriptome remodeling of Arabidopsis in response to high levels of magnesium sulfate

status: Public on Sep 17 2010

city: Gainesville

first: Anne

last: Visscher

state: FL

address: Fifield Hall

department: Horticultural Science

institute: University of Florida

summary: Martian regolith (unconsolidated surface material) is a potential medium for plant growth in bioregenerative life support systems during manned missions on Mars. However, hydrated magnesium sulfate mineral levels in the regolith of Mars can reach as high as 10 wt%, and would be expected to be highly inhibitory to plant growth. A global approach was used to identify novel genes with potential to enhance tolerance to high MgSO4 stress. The early Arabidopsis root transcriptome response to elevated concentrations of magnesium sulfate was characterized in col-0, and also between col-0 and the mutant line cax1-1 – a mutant relatively tolerant of high levels of MgSO4•7H2O in soil solution.

overall_design: After 3 weeks of growth under hydroponic conditions, Arabidopsis thaliana col-0 roots were exposed to a basic nutrient solution (0.25 g/L MES, 1/16x MS, pH 5.7) with an additional 2.08 mM magnesium sulfate (total Ca:Mg ratio = 1:15) for 45 min., 90 min., or 180 min., while a col-0 control set was exposed to the basic nutrient solution without additional magnesium sulfate for 45 minutes. Arabidopsis thaliana cax1-1 roots were exposed to the basic nutrient solution with additional magnesium sulfate for 180 min. only. Four replicate containers were harvested for the control and each of the treatment sets, resulting in a total of 20 samples. Gene expression of the col-0 sets exposed to magnesium sulfate treatment for 45 min., 90 min., or 180 min. was compared to gene expression of the col-0 control set. Gene expression of the cax1-1 set exposed to magnesium sulfate treatment for 180 min. was compared to gene expression of the col-0 set exposed to magnesium sulfate treatment for 180 minutes.

first: Anna-Lisa

last: Paul

first: Robert

middle: J

last: Ferl

first: Matias

last: Kirst

first: Charles

last: Guy


title: Mouse tissue-resident macrophage expression profiles

status: Public on Sep 22 2010

city: South San Francisco

first: Yan

last: Ma

address: 1 DNA Way

department: Bioinformatics

institute: Gentech Inc

summary: We show that macrophages from murine spleen, liver and peritoneum display dramatically different expression profiles. Clusters of genes were found to represent unique biological functions related to adhesion, antigen presentation, phagocytosis, lipid metabolism and signal transduction. Some gene families, such as integrins, are differentially expressed among the macrophages resident in different tissues, suggesting that the tissue of residence influences their biological function.

overall_design: 18 FACS sorted mouse tissue-resident macrophge samples. 6 cell types, 3 biological replicates per cell type.

first: Hilary

middle: F

last: Clark

first: Nick

middle: N

last: Gorgani


title: Menopause and diabetes effect on kidney cortex

status: Public on Sep 14 2010

city: Tucson

first: Heddwen

last: Brooks

state: AZ

address: PO Box 245218 1656 E Mabel

institute: University of Arizona

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

overall_design: Refer to individual Series


title: Genetic and epigenetic characteristics of human multiple hepatocellular carcinoma

status: Public on Sep 09 2010

city: Osaka

first: Kikuya

last: Kato

address: 1-3-3 Nakamichi, Higashinari-ku

institute: Osaka Medical Center for Cancer and Cardiovascular Dieseases

summary: Multiple carcinogenesis is one of the major characteristics of human hepatocellular carcinoma (HCC). The history of multiple tumors, i.e., whether they are derived from a common precancerous or cancerous ancestor or individually from hepatocytes, is a major issue. Multiple HCC is clinically classified into intratumor metastasis (IM) and multicentric carcinogenesis (MC). Molecular markers differentiating IM and MC are of interest to clinical practitioners because clinical diagnosis of IM and MC often leads to different therapies. We analyzed multiple HCCs for somatic mutations of cancer-related genes, chromosomal aberrations, and promoter methylation of tumor suppressor genes, using techniques such as high-resolution melting, array-comparative genomic hybridization (CGH), and quantitative methylation-specific PCR.

overall_design: Comparative genomic hybridizaion experiments. A total of 20 tumor samples: ten pairs of HCC (from ten patients).

first: Kazuya

last: Taniguchi


title: Williams-Beuren syndrome: typical deletions versus atypical deletions of the 7q11.23 region

first: Anna

last: Antonell

address: C/Casanova, 143

department: Unitat d'Alzheimer i altres transtorns cognitius

institute: Hospital Clínic Barcelona

summary: We have performed comparative transcriptome profile from lymphoblastoid cell lines from four Williams-Beuren syndrome patients and two patients with partial deletions of the region. The goal was to find deregulated genes specifically in WBS versus atypical deletions, and to determine the biological pathways affected in WBS patients.

overall_design: 6 samples were hybridized twice each: once labeled with Cy5 and once labeled with Cy3 (dye-swap). Each sample was hybridized against a pool of five controls of the same gender.

first: Mireia

last: Vilardell

first: Alberto

last: Pérez-Jurado


title: Zic3 ChIP-on-chip in mouse ES cells

status: Public on Sep 13 2010

city: Singapore

first: Linda

middle: Shushan

last: Lim

address: 60 Biopolis Street, Genome building, #02-01

department: Stem Cell Biology

country: Singapore

institute: Genome Institute of Singapore

type: Genome binding/occupancy profiling by genome tiling array

summary: The transcription factor Zic3 is required for maintenance of embryonic stem (ES) cell pluripotency (Lim LS et al, Mol Biol Cell. 2007;18:1348-1358). By genome-wide chromatin immunoprecipitation (ChIP-chip) in ES cells, we have identified 379 direct Zic3 targets, many of which are functionally associated with pluripotency, cell cycle, proliferation, oncogenesis and early embryogenesis.

overall_design:
E14 cells were cultured to a density of 1 x 108 cells for each IP. Two biological replicates were performed per experiment. Cells were cross-linked for 10 minutes at room temperature with 1% (w/v) formaldehyde and the reaction subsequently quenched with 125mM glycine. Nuclear fractions were isolated and the DNA sheared to average lengths of 200-500 bp.

For analysis on mouse promoter arrays, purified ChIP material was processed according to the Agilent ChIP-on-chip protocol, and labeled DNA was hybridized to Agilent mouse promoter ChIP-on-chip arrays for 40 hours at 65oC (G4490A; Agilent Technologies, Santa Clara, CA). Chips were washed and scanned as per manufacturer’s protocol and the results were processed with Agilent's ChIP Analytics software v1.3. A p-value cutoff <0.001 was specified in our analysis. To further minimize false positives, we applied a “neighborhood voting” algorithm [2] to filter for high confidence Zic3-enriched sites, wherein binding was considered genuine only in the presence of a second, significantly enriched, neighboring probe (p < 0.005).

first: Galih

last: Kunarso

first: Felicia

last: Hong

first: Lawrence

middle: W

last: Stanton


title: Acute lymphoblastic leukemia

status: Public on Sep 10 2010

city: St. Peter

first: Sanjive

last: Qazi

address: 800 west College Av

department: Biology

institute: Gustavus Adolphus College

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Regional Immune Response to Trichostrongylis colubriformis in Sheep

status: Public on Sep 01 2010

city: Puddle Alley

first: Alan

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ


title: Cultured OEC versus cultured SC and versus native OEC

status: Public on Nov 02 2010

first: Kasper

middle: Cornelis Dammes

last: Roet

address: Meibergdreef 47

department: Neuroregeneration

institute: Netherlands Institute for Neuroscience

summary: This microarray study aimed at identifying the differences in the global gene expression growth program of adult cultured olfactory ensheathing cells (cOEC) (from the olfactory bulb) versus adult cultured Schwann cells (SC) (from the sciatic nerve) and versus adult OEC directly dissected from the olfactory nerve layer (nOEC). The aim of the comparison between cOEC and SC is to define intrinsic molecular differences that distinguish cOEC from SC (both cell types support neuronal regeneration). The aim of the comparison between cOEC and nOEC is to determine the transcriptional responses that are induced in OEC during culturing.

overall_design: Three-condition experiment: cOEC vs. SC, cOEC vs. nOEC, SC vs. nOEC. Biological replicates: 3 cOEC-SC replicates, 3 cOEC-nOEC replicates, 3 SC-nOEC replicates. A factorial design was used consisting of direct comparisons between the three cell types (Glonek and Solomon, 2004 (PMID 14744830).

first: E

last: Franssen

first: F

last: De Bree

first: K

middle: C


title: CGH validation of de novo CNVs in asthma and CEU HapMap samples

city: Seattle

first: Andy

last: Itsara

state: WA

address: Foege Building S-250, Box 355065, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington School of Medicine

type: Genome variation profiling by genome tiling array


title: Consequences of an in utero TCDD exposure on the male reproductive function in 5 and 28 postnatal days rat

status: Public on Dec 01 2010

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France


title: Global regulation in response to sulfur availability in the cheese-related bacterium, Brevibacterium aurantiacum

status: Public on Nov 25 2010

city: Thiverval-Grignon

first: Marie-Pierre

last: FORQUIN

address: Aveniue de la Bretigniere

department: MICA

institute: INRA

summary:
In this study, we combined metabolic reconstruction, growth assays, metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in Brevibacterium aurantiacum. In agreement with the growth of B. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway and of thiolation pathways that produce cysteine (cysE and cysK) or homocysteine (metX and metY) from sulfide, of at least one gene of the transsulfuration pathway (aecD) and of genes encoding three MetE-type methionine synthases. We also compared the expression profiles of B. aurantiacum ATCC9175 during sulfur starvation and in the presence of sulfate, cystine or methionine plus cystine. In sulfur starvation, 690 genes including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in presence of cysteine, while the expression of metX, metY, metE1, metE2 and BL613 encoding a probable cystathionine-γ-synthase decreased in the presence of methionine. We identified three ABC transporters: two stronger transcribed during cysteine limitation and one during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase, BL929, and a methionine transporter (metPS) was induced in the presence of methionine, in conjunction with a significant increase of volatile sulfur compounds production.

This SuperSeries is composed of the SubSeries listed below.

last: Forquin

first: Caroline

last: Proux


title: Body size regulation and TGF-beta Sma/Mab pathway: sma L4 vs N2 L4

city: Princeton

first: Shijing

last: Luo

state: NJ

address: 160 Carl Icahn Lab, Princeton University

institute: Princeton University

summary: To find genes downstream of the TGF-beta Sma/Mab pathway associated with body size regulation in C. elegans.

overall_design: Three replicates comparing RNA from sma-2(e502) L4 whole animal with RNA from wild-type L4 whole animal, in which one is dye flipped. Plus one array comparing RNA from sma-4(e729) L4 whole animal with RNA from wild-type L4 whole animal.

first: Wendy

last: Shaw

first: Coleen

middle: T

last: Murphy


title: Reproductive aging: fem-1 day 3 oocyte vs fem-1 day 8 oocyte

summary: To find genes in C. elegans oocytes associated with reproductive aging.

overall_design: Five replicates comparing RNA from oocyte samples collected from day 3 fem-1(hc17) animals with RNA from oocyte samples collected from day 8 fem-1(hc17) animals. Three out of five are dye-flipped.


title: Reproductive aging: sma-2;fem-1 day 8 oocyte vs fem-1 day 8 oocyte

summary: To find genes downstream of the TGF-beta Sma/Mab pathway in C. elegans oocytes associated with reproductive aging.

overall_design: Eight replicates comparing RNA from oocyte samples collected from day 8 sma-2(e502);fem-1(hc17) animals with RNA from oocyte samples collected from day 8 fem-1(hc17) animals. Five out of eight are dye-flipped.


title: Gene expression and single feature polymorphisms in xylem tissue on an Eucalyptus pseudo-testcross population

status: Public on Sep 18 2010

first: Leandro

middle: Gomide

last: Neves

address: 2033 Mowry Road

department: Plant Molecular and Cell Biology

type:
Expression profiling by array
Other

sample_organism: Eucalyptus grandis x Eucalyptus urophylla


title: Altered Gene Expression in Human Adipose Stem Cells Cultured with Fetal Bovine Serum Compared to Human Supplements

status: Public on Aug 28 2010

city: Mannheim

first: Karen

last: Bieback

address: Ludolf-Krehl-Strasse 13-17

institute: Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University

summary: Mesenchymal stromal cells (MSCs) are promising candidates for innovative cell therapeutic applications. For clinical scale manufacturing regulatory agencies recommend to replace fetal bovine serum (FBS) commonly used in MSC expansion media as soon as equivalent alternative supplements are available. We already demonstrated that pooled blood group AB human serum (HS) and thrombin-activated platelet releasate plasma (tPRP) support the expansion of multipotent adipose tissue-derived MSCs (ASCs). Slight differences in size, growth pattern and adhesion prompted us to investigate the level of equivalence by compiling the transcriptional profiles of ASCs cultivated in these supplements. A whole genome gene expression analysis was performed and data verified by PCR and protein analyses. Microarray-based screening of 34,039 genes revealed 102 genes differentially expressed in ASCs cultured with FBS compared to HS or tPRP supplements. A significantly higher expression in FBS cultures was found for 90 genes (fold change .2). Only 12 of the 102 genes showed a lower expression in FBS compared to HS or tPRP cultures (fold change .0.5). Differences between cells cultivated in HS and tPRP were hardly evident. Supporting previous observations of reduced adhesion of cells cultivated in the human alternatives we detected a number of adhesion and extracellular matrix associated molecules expressed at lower levels in ASCs cultivated with human supplements. Confirmative assays analysing transcript or protein expression with selected genes supported these results. Likewise a number of mesodermal differentiation associated genes were higher expressed in cells grown in FBS. Quantifying adipogenic and osteogenic differentiation lacked to demonstrate a clear correlation to the supplement due to donor-sepcific variances. Our results emphasize the necessity of comparability studies as they indicate that FBS induces a culture adaptation exceeding that of ex vivo culture in human supplements and thus may contribute to the therapeutic potential.

overall_design: Microarray hybridizations (Agilent: Whole Human Genome Oligo Microarray; 41k unique probe) were carried out with 5 µg Cy3 labeled cRNA and 5 µg Cy5 labeled cRNA, both prepared from each sample.

first: Viet-Anh-Thu

last: Ha

first: Andrea

last: Hecker

first: Melanie

last: Grassl

first: Sven

last: Kinzebach

first: Hermann

last: Solz

first: Carsten

last: Sticht

first: Harald

last: Klüter

first: Peter

last: Bugert


title: TGF-beta Sma/Mab signaling regulates a set of genes in oocytes associated with reproductive aging and another set in L4 associated with body size growth

summary:
Reproductive cessation is perhaps the earliest aging phenotypes humans experience. Similarly, C. elegans' reproduction ceases in mid-adulthood. Although somatic aging has been studied in both worms and humans, mechanisms regulating reproductive aging are not yet understood. Here we show that TGF-beta Sma/Mab activity regulates reproductive aging transcriptionally separable from its regulation of body size growth.

This SuperSeries is composed of the SubSeries listed below.


title: Diurnal Regulation of Gene Expression in Leaves and Immature Ears Over a 72-Hour Period

status: Public on Sep 02 2010

city: Johnston

first: Kevin

middle: Robert

last: Hayes

state: IA

address: 7200 NW 62nd Ave

institute: Pioneer Hi-Bred International


title: Gene copy number variation in male breast cancer by aCGH

city: Bari

first: Pina

last: Iannelli

address: viale Orazio Flacco, 65

country: Italy

institute: National Cancer Centre "Giovanni Paolo II"

summary: Characterization of DNA imbalances in a set of 25 MBC samples analyzed by high resolution CGH arrays in order to detect DNA copy number aberrations (CNAs). These results have been then compared with a female breast cancer dataset deposited with the Gene Expression Omnibus.

overall_design:
Male patients affected by breast cancer have been consecutively selected for this retrospective study: 15 received the primary diagnosis of breast cancer at the NCC of Bari, while 10 at Regina Elena Institute of Rome, Italy.
This dataset was compared to GSE12659 (female breast cancer).

first: Stefania

last: Tommasi

first: Anita

last: Mangia

first: Giuseppina


title: Gene Expression Profiling Identifies Inflammation and Angiogenesis as Distinguishing Features of Canine Hemangiosarcoma

status: Public on Aug 24 2010

city: Denver

first: Beth

last: Tamburini

address: 1400 Jackson Street, K503

department: Immunology

institute: University of Colorado Denver

summary:
Background
The etiology of hemangiosarcoma remains incompletely understood. Its common occurrence in dogs suggests predisposing factors favor its development in this species. These factors could represent a constellation of heritable characteristics that promote transformation events and/or facilitate the establishment of a microenvironment that is conducive for survival of malignant blood vessel-forming cells. The hypothesis for this study was that characteristic molecular features distinguish hemangiosarcoma from non-malignant endothelial cells, and that such features are informative for the etiology of this disease.
Methods
We first investigated mutations of VHL and Ras family genes that might drive hemangiosarcoma by sequencing tumor DNA and mRNA (cDNA). Protein expression was examined using immunoblotting. Next, we evaluated genome-wide gene expression profiling using the Affymetrix Canine 2.0 platform as a global approach to test the hypothesis. Data were evaluated using routine bioinformatics and validation was done using quantitative real time RT-PCR.
Results
Each of 10 tumor and four non-tumor samples analyzed had wild type sequences for these genes. At the genome wide level, hemangiosarcoma cells clustered separately from non-malignant endothelial cells based on a robust signature that included genes involved in inflammation, angiogenesis, adhesion, invasion, metabolism, cell cycle, signaling, and patterning. This signature did not simply reflect a cancer-associated angiogenic phenotype, as it also distinguished hemangiosarcoma from non-endothelial, moderately to highly angiogenic bone marrow-derived tumors (lymphoma, leukemia, osteosarcoma).
Conclusions
The data show that inflammation and angiogenesis are important processes in the pathogenesis of vascular tumors, but a definitive ontogeny of the cells that give rise to these tumors remains to be established. The data do not yet distinguish whether functional or ontogenetic plasticity creates this phenotype, although they suggest that cells which give rise to hemangiosarcoma modulate their microenvironment to promote tumor growth and survival. We propose that the frequent occurrence of canine hemangiosarcoma in defined dog breeds, as well as its similarity to homologous tumors in humans, offers unique models to solve the dilemma of stem cell plasticity and whether angiogenic endothelial cells and hematopoietic cells originate from a single cell or from distinct progenitor cells.

This SuperSeries is composed of the SubSeries listed below.


title: Mouse placenta in spontaneous abortion

status: Public on Aug 21 2010

city: Izumisano, Osaka

first: Ken

last: Kusakabe

address: 1-58 Rinku-ourai Kita

institute: Osaka Prefecture University

summary: Genetic profiles of mouse placenta were examined especially at the implantation sites of causing spontaneous abortion at day 14.5 of pregnancy. There is a number of the suffered patients from the recurrent spontaneous abortion by unknown causes. It is an important process to   understand genetic profiles in the abortion placentas for the investigation of specific causes to induce rejection of normal embryos from the maternal attack. Our study was carried out on the laboratory mice targeted spontaneous abortion to approximate human disease models.

overall_design: Three samples from the each implantation site of normal and abortion in the same pregnant uterus.


title: Generation of induced pluripotent stem cells in rabbits: potential experimental models for human regenerative medicine

status: Public on Jul 28 2010

city: Tsukuba

first: Arata

last: Honda

institute: RIKEN BRC

summary: Human induced pluripotent stem (iPS) cells have the potential to establish a new field of promising regenerative medicine. Therefore, the safety and the efficiency of iPS-derived cells must be tested rigorously using appropriate animal models before human trials can commence. Here, we report the establishment of rabbit iPS cells as the first human-type iPS cells generated from a small laboratory animal species. Using lentiviral vectors, four human reprogramming genes (c-MYC, KLF4, SOX2 and OCT3/4) were introduced successfully into adult rabbit liver and stomach cells. The resulting rabbit iPS cells closely resembled human iPS cells; they formed flattened colonies with sharp edges and proliferated indefinitely in the presence of bFGF. They expressed the endogenous pluripotency markers c-MYC, KLF4, SOX2, OCT3/4 and NANOG, while the introduced human genes were completely silenced. Using in vitro differentiating conditions, rabbit iPS cells readily differentiated into ectoderm, mesoderm and endoderm. They also formed teratomas containing a variety of tissues of all three germ layers in immunodeficient mice. Thus, the rabbit iPS cells fulfilled all of the requirements for the acquisition of the fully reprogrammed state, showing high similarity to their embryonic stem (ES) cell counterparts we generated recently. However, their global gene expression analysis revealed a slight, but rigid difference between these two types of rabbit pluripotent stem cells. The rabbit model should enable us to compare iPS cells and ES cells under the same standardized conditions in evaluating their ultimate feasibility for pluripotent cell-based regenerative medicine in humans.

overall_design: Comparison of rabbit embryonic stem cells, rabbit somatic cells, and rabbit induced pluripotent stem cells at several timing (passage number 6, 7, 22, 23) of cultures. Eight samples were used for assessment.


title: Multiple chromosomal monosomies are characteristic of giant cell ependymoma

status: Public on Aug 30 2010

city: Oslo

first: Hanne-Sofie

middle: S

last: Dahlback

address: Montebello

department: Section for Cancer Cytogenetics

country: Norway

institute: The Norwegian Radium Hospital

summary: Giant cell ependymoma (GCE), a rare ependymoma subtype, was only recently recognised as a separate diagnostic entity with variations both in malignant potential and in course of disease. The pathogenetic mechanisms behind ependymomas remain unknown. Only one karyotyped GCE has so far been reported. We present the first genomic characterisation of a supratentorial GCE using G-band karyotyping, DNA ploidy analysis and array comparative genomic hybridisation (aCGH). The G-banded karyotype was hypodiploid with multiple monosomies, a feature present also in the previously published case and, hence, probably characteristic of these tumours. We could also analyse cytogenetically a subsequent recurrent tumour, phenotypically an anaplastic ependymoma, but exhibiting a pattern of monosomies largely similar to that found in the primary tumour, allowing a first insight into the genetic events involved also in disease progression.

overall_design: 2 tumour samples analysed with the control DNA (supplied by Agilent)

first: Petter

last: Brandal

first: Bård

middle: K

last: Krossnes

first: Radec

last: Fric

first: Torstein

last: Meling

first: Leonardo

middle: A

last: Meza-Zepeda

first: Håvard

last: Danielsen

first: Sverre

last: Heim


title: Viral Microarray

status: Public on Aug 23 2010

city: New York

first: Omar

last: Jabado

address: 722 W 168 Street 17th Fl

department: Epidemiology

institute: Columbia University

sample_organism: Influenza A virus (A/Texas/36/1991(H1N1))


title: Gene regulation in osmpk6 mutant cells expressing OsMKK4DD

status: Public on Jul 30 2010

first: Hirohiko

last: Hirochika

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Genome and Biodiversity Research

institute: National Institute of Agrobiological Sciences

summary: OsMKK4 is a rice MAPKK and immediately activated by treatment with chitin elicitor, a fungal MAMP. OsMKK4 phosphrylate and activate OsMPK6. We compared gene expression in osmpk6 and osmpk6 complemented cells expressing active OsMKK4 using rice 44K oligoarray.

overall_design: We used transgenic osmpk6 mutant and osmpk6 complemented callus expressing active OsMKK4 (OsMKK4DD) under the dexamethazone (DEX)-inducible promoter. Callus were treated with DEX or control ethanol. Samples were derived from 3 biological replicates and labeled by one-color method.

first: Mitsuko

last: Kaboshi

first: Akira

last: Takahashi


title: Comparison Between Gene Expression Profiles of Sensitive and Resistant Trabectedin Liposarcoma Cell Lines

status: Public on Jul 13 2010

city: Milano

first: Luca

last: Clivio

address: via La Masa 19

institute: Istituto di Ricerche Farmacologiche Mario Negri

summary: Gene expression profiles of 402-91 FUS-CHOP type I cells have been compared to 402-91/ET cells made resistant to Trabectedin

overall_design: Experiments were performed on purified RNA from independent batches of 402-91 and 402-91/ET cells without drug treatment.

first: Annapaola

last: Santarsiero

first: Sergio

last: Marchini

first: Giovanna

last: Chiorino


title: Changes in gene expression induced by apple polyphenol (APP)

status: Public on Aug 10 2010

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

state: MT

address: 960 Technology Blvd.

department: Veterinary Molecular Biology

institute: Montana State University

summary:
γδ T cells are lymphocytes that function in both innate and adaptive immune responses, and our laboratory has previously reported that both bovine and human γδ T cells are primed for secondary responses by tannin components of the unripe apple peel (APP).  In this report we began to investigate the mechanism by which priming occurs.  We performed a microarray analysis on sorted bovine γδ T cells treated with APP and observed significant increases in transcripts encoding select inflammatory cytokines, such as GM-CSF, IL-8, and IL-17, but not markers of TCR stimulation such as IFNγ.  When injected into the gut of mice, APP induced a robust influx of neutrophils into both the blood and peritoneum as measured by FACS.  Importantly, both GM-CSF and IL-8 proteins were detected in these animals.  Further studies were performed using the human γδ T cell-line MOLT-14, as large numbers of cells were required for subsequent experiments.   Using these cells we found that both the GM-CSF and IL-8 mRNAs were significantly upregulated and stabilized in cells treated with APP.  Finally, we show that the ERK1/2 MAPK pathway was activated in APP-treated MOLT-14 cells, and that this pathway plays a role in the mRNA stabilization we observed.  Together, our data describe a unique inflammatory response in bovine, murine, and human γδ T cells in response to APP, and suggest that mRNA stability mechanisms could account for the priming phenotype we previously observed.APP has a distinctive gamma delta T cells specific priming activity.

Keywords: comparison of 2 treatment types, tannin, gamma delta T cells

overall_design: To begin to understand the effects of APP in innate immunity, we investigated the global gene expression profiles of stimulated bovine gamma delta T cells.  Peripheral blood from 2 neonatal bovine calves was collected.  gamma delta T cells were sorted to >97% purity using a FACS Vantage.  Cells were placed in culture and stimulated with either an aqueous extract of APP (42.2ug/ml) or PBS for 4 hours after which RNA was extracted and processed for microarray analysis following standard protocols from Affymetrix.

first: Katie

last: Daughenbaugh


title: Transcriptomic comparison of fructose and lipid grown cultures of Ralstonia eutropha H16

status: Public on Aug 27 2010

city: Cambridge

first: Christopher

middle: John

last: Brigham

state: MA

address: 31 Ames Street

institute: Massachusetts Institute of Technology

summary: Whole genome gene expression analysis was examined with Ralstonia eutropha strain H16 cultures grown in PHB production medium (recipe per Peoples and Sinskey, 1989) containing fructose or trioleate as the main carbon source.  The goal of this analysis was to determine the identity of the triacylglycerol and fatty acid breakdown genes in R. eutropha strain H16.

sample_organism:
Cupriavidus necator
Cupriavidus necator H16

overall_design: In the study presented here, triplicates of R. eutropha strain H16 were examined for changes in expression of 6702 genes during growth and PHB production on each carbon source.

first: Jason

last: Holder

first: Qiandong

last: Zheng

first: Charles

last: Budde

first: Alison

last: Mahan

first: Stuart

last: Levine

first: Manlin

last: Luo

first: Allison

last: Perrotta


title: Long noncoding RNA as modular scaffold of histone modification complexes

status: Public on Jul 08 2010

city: Stanford

first: Miao-Chih

last: Tsai

state: CA

address: 269 Campus Drive, CCSR 2140

institute: Stanford University

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

overall_design: Refer to individual Series


title: Subunit-specific vs. non-selective proteasome modulation in limiting inflammation in experimental colitis

status: Public on Jul 07 2010

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Inflammatory bowel disease (IBD), comprising Crohn´s disease and Ulcerative colitis, is characterized by chronic relapsing inflammation of the gut. It has been shown that increased proteasomal activity is associated with the expression of immunoproteasomes, which enhances NF-kB activation and thus promotes inflammation in IBD-patients. Here, we investigate whether modulation of the proteasomal activity is a suitable therapeutic approach to limit inflammation in colitis. This concept was tested in two different experimental setups. First, development of dextran sulfate sodium (DSS)-induced colitis was tested in lmp7-/--mice, which lack the essential immunoproteasome-subunit LMP7 or in wildtype-mice treated with the proteasome inhibitor bortezomib. Compared to WT mice, lmp7-/- mice revealed significantly attenuated colitis resulting from reduced NF-kB activation in the absence of LMP7. Further, treatment with bortezomib revealed dose-dependent amelioration of DSS-induced inflammation. In both approaches proteasome modulation limited the infiltration of neutrophils, consequently reducing tissue damage. In summary our experiments demonstrate that modulation of the proteasomal activity is effective in attenuating experimental colitis. In particular, our data suggest that the immunoproteasome-subunit LMP7 is a suitable target for the therapy of IBD.

overall_design: Microarray experiments were performed as dual-color hybridizations. To compensate for dye-specific effects, a dye-reversal color-swap was applied. Samples of proximal colon were cut longitudinally, washed in PBS, shortly incubated in 4M Guanidinium-isothiocyanat and transferred to TRIzol (Invitrogen).

first: Nicole

last: Schmidt

last: Molenkopf

first: Stefan

last: Kaufmann

first: Ulrich

last: Steinhoff

first: Thorsten

last: Joeris


title: Multi-Targeted Priming For Genome-Wide Gene Expression Assays

status: Public on Jul 20 2010

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

sample_organism:
Saccharomyces cerevisiae
Neurospora crassa


title: Conditional Dmrt1 knockout gene expression

status: Public on Jun 30 2010

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota


title: Expression profiling of the heat stress response in acclimated and unacclimated peanut

city: Lubbock

first: Kameswara Rao

last: Kottapalli

state: TX

address: 3810 4th Street

department: Plant & Soil Science

institute: USDA-ARS Lubbock & Texas Tech University


title: Prostaglandin F2α -induced changes in transcriptome of bovine mid cycle versus early corpus luteum

status: Public on Jul 31 2010

city: East Lansing

first: juan

middle: p

last: steibel

state: MI

address: 1205 I Anthony Hall

institute: Michigan State University

summary: Despite much investigation, mechanisms conferring stage specific responsiveness of the corpus luteum (CL) to prostaglandin F2 (PG) are unknown. The objective of this study was to identify PG- induced changes in transcriptome of bovine CL specific to d 11 ( PG responsive) but not d 4 (PG refractory) CL associated with luteolysis. CL were collected from heifers at 0, 4 and 24 h following PG injection on d 4 and 11 of the estrous cycle (n = 5 animals/treatment) and isolated RNA labeled and hybridized to Affymetrix GeneChip Bovine Genome Arrays.   At 4 and 24 h post PG respectively, 221 (d 4) and 661 (d 11) and 248 (d 4) and 1419 (d 11) regulated genes were identified.

overall_design: Thirty Angus crossbred heifers were assigned to one of six treatments (n = 5 per treatment) in a 2 x 3 factorial arrangment, using a completely random design.Corpora lutea were collected at 0 (control), 4 or 24 h following injection of saline (control) or PG on d 4 or d 11 of the estrous cycle.  Total RNA was isolated from luteal tissue. The isolated RNA was labeled and hybridized to Affymetrix GeneChip Bovine Genome Arrays.

first: Mohan

last: Mondal

first: Beau

last: Schilling

first: Joe

last: Folger

first: Juan

middle: P

last: Stiebel

first: James

last: Ireland

first: Rina

last: Meidan

first: George

last: Smith


title: Genome-wide analysis of in-trans correlations between copy number and expression with application to human breast cancer

status: Public on Jul 01 2010

first: Jørgen

middle: Mømb

last: Aarøe

department: Genetics

summary:
Background: Genomic instability is a hallmark of cancer and is frequently reflected in the DNA copy number profile and the expression profile of genes. Methodology is needed to compare array-CGH data and microarray expression data in order to unveil effects of DNA copy number alterations of a gene on the expression of the gene itself (in-cis effects) and on other genes (in-trans effects).
Results: We present a method for detection of gene dosage effects on gene expression that first searches for genome-wide in-cis associations between copy number and expression, and then investigates in-trans effects of these genes. A key element of the method is a correction step to eliminate potential confounding effects of in-cis associations when searching for in-trans associations. This facilitates reliable detection of local in-trans associations (i.e. associations within a chromosome) and alleviates the problem of co-occurring copy number aberrations across the genome. Applying the method to data collected from breast carcinomas from 20 women, we found 422 genes with expression levels that are highly correlated to DNA copy number (in-cis) in certain regions of the genome. Of these, 109 (26%) had significant trans-correlation with the expression levels of a large number of genes (20 or more). The strongest trans-regulators were also differentially expressed in subgroups that were found on the basis of expression data by classification of the tumors to previously defined breast cancer subtypes. A study of the most significant in-trans correlated genes yields significant enrichment of certain cancer related pathways and GO terms.
Conclusions: We introduce a method for the joint comparative analysis of expression and copy number profiles for the discovery and investigation of in-cis and in-trans regulatory mechanisms. Using data from 20 primary human breast cancers, a number of significant in-trans regulatory genes were found and their biological relevance indicated, calling for the application of the methods on larger data sets.
Keywords: Correlations between copy number and gene expression, breast cancer

overall_design:
Patient samples:
From May 1995 to December 1998, 920 patients referred for surgical treatment of breast cancer from five different hospitals in the Oslo region entered into a large study on detection and evaluation of isolated tumor cells in bone marrow. From theses 920 patients, fresh frozen tumor tissue samples from 20 patients were selected for this study. All 20 breast carcinomas contained >40% tumor cells, the majority of the tumor specimens represent tumor size T1/T2, node status N0/N1 (9/11) and histological grade 2 or 3. The 20 samples have been classified into five clinically relevant molecular tumor subclasses, based on their expression profile. Each sample was analyzed on both CGH- and gene expression microarrays (no replicates). All experiments were conducted at The Norwegian Radium Hospital.
Array CGH experiments:

Agilent's Human Genome CGH Microarray 44A contains 44,255 in situ synthesized 60-mer probes (3,877 controls) designed for studying copy number changes and representing most of the known or predicted human genes. The probes are, according to manufacturers description, enriched for cancer relevant genes representing both coding and non-coding sequences on the chromosomes.

Gene expression experiments:
Agilent Whole Human Genome Oligo Microarrays containing ~44,000 oligonucleotide probes were used for the gene expression experiments, according to manufacturer’s protocol.

first: Lars

middle: O

last: Baumbusch

first: Doron

last: Lipson

middle: M

first: Anya

last: Tsalenko

first: Bjørn

last: Naume

first: Knut

last: Liestøl

first: Zohar

last: Yakhini

first: Ole

last: Lingjærde

first: Anne-Lise

last: Børresen-Dale


title: Global gene expression analysis in the pedicel abscission zone of tomato flowers by DNA microarray

status: Public on Jul 03 2010

first: Yasuhiro

last: Ito

address: 2-1-12 Kannondai

department: Food Biotechnology Division

institute: National Food Research Institute

summary: In tomato, the mutants that lack the abscission zone (AZ) within pedicels are called a ‘jointless’ and are agronomically significant in that they increase the tomato fruit yield for industrial processing. We have employed  DNA microarray expression analysis to identify genes with the potential to play a role in development of the pedicel abscission zone of tomato, and identified several classes of differentially regulated genes between pedicels of the AZ-forming line (wild-type) and pedicels of the non AZ-forming lines (jointless mutant and MC-suppressed transformant).

overall_design: Tomato flower pedicels were harvested at anthesis stage from the AZ-forming line (wild-type) and the non AZ-forming lines (jointless mutant and MC-suppressed transformant), and subjected to DNA microarray analyses.  Experiments were performed twice with independently prepared samples.

first: Toshitsugu

last: Nakano

first: Junji

last: Kimbara

first: Masaki

last: Fujisawa

first: Mamiko

last: Kitagawa

first: Nao

last: Ihashi

first: Takafumi

last: Kasumi


title: Drosophila melanogaster miR310 cluster over-expression and knockout

status: Public on Jun 25 2010

city: Guangzhou

first: TIAN

last: TANG

address: Xingangxi Rd. #135

institute: Sun Yat-Sen University

type: Expression profiling by genome tiling array

summary:
We tested and measured the strength of heterospecific interactions between microRNAs and their targets by carrying out transgenic experiments across Drosophila species, by over-expressing the miR310s cluster of D. melanogaster (Dm310s) and D. pseudoobscura (Dp310s) in D. melanogaster. A knockout line, referred to as Dm310s (−), was also included for comparison. The whole-genome expression (WGE) of the Dp310s and Dm310s transgenic lines were compared on two platforms of both Affymetrix tiling array and DGRC cDNA array. The WGE of knockout line was assayed on only Affymetrix tiling array. In the Dm310s lines, overexpression was more common than underexpression among misregulated genes while the pattern appeared to be reversed in the Dm310s(−) line. The number of genes significantly misexpressed under the influence of Dp310s is 3-10 times greater than under Dm310s.  Importantly, the numbers of predicted targets are similar between them.  Expression analysis of the predicted target genes suggests that miRNAs may sometimes function to buffer fluctuations in the transcriptome output.  After the buffering function has evolved, heterospecific combinations may cause adverse effects.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
The three data sets are all parts of the same overall study, in which we over-expressed the Dm310s and Dp310s in D. melanogaster, and analyzed the transcriptional consequences by using microarrays. A knockout line was also used to provide supplementary information.
For more details, refer to individual Series.


title: Genome-wide location analysis of Dnmt3a-mediated epigenetic regulation in murine postnatal subventricular zone (SVZ) neural stem cells (NSCs) [Agilent]

city: Los Angeles

first: Yi

last: Sun

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

summary: DNA methylation at proximal promoters facilitates lineage restriction by silencing cell-type specific genes. However, euchromatic DNA methylation frequently occurs in regions outside promoters. The functions of such non-proximal promoter DNA methylation are unclear. Here we show that the de novo DNA methyltransferase Dnmt3a is expressed in postnatal neural stem cells (NSCs) and is required for neurogenesis. Genome-wide analysis of postnatal NSCs indicates that Dnmt3a occupies and methylates intergenic regions and gene bodies flanking proximal promoters of a large cohort of transcriptionally permissive genes, many of which encode regulators of neurogenesis. Surprisingly, Dnmt3a-dependent non-proximal promoter methylation promotes expression of these neurogenic genes by functionally antagonizing Polycomb repression. Thus, non-promoter DNA methylation by Dnmt3a may be utilized for maintaining active chromatin states of genes critical for development.

overall_design: Chromatin extracted from wild-type (WT) or Dnmt3a-null (KO) SVZ NSCs was immunoprecipitated with indicated antibodies and analyzed by Agilent 244K extended promoter (-5.5kb to +2.5kb flanking transcription start sites) microarrays. Whole cell extract (WCE) was used as input controls for most experiments (IP/WCE). For other experiments, immunoprecipitated DNA from WT and KO NSCs was directly compared on the same microarrays (IP/IP).

first: Hao

last: Wu

first: Volkan

last: Coskun

first: Jifang

last: Tao

first: Wei

last: Xie

first: Weihong

last: Ge

first: Kazuaki

last: Yoshikawa

first: En

last: Li

last: Zhang

middle: E


title: LCM-based microarray analysis of TAU-P301L and SOD1-G93A motor neurons and surrounding glial cells

status: Public on Jun 24 2010

city: Torrance

first: Stanislav

middle: L

last: Karsten

address: 1124 West Carson Street

department: Neurology

institute: UCLA School of Medicine

summary: Familial amyotrophic lateral sclerosis (ALS) represents about 10% of ALS cases. In about 20% of familial ALS patients, a mutation in superoxide dismutase-1 (SOD1) can be found. The ubiquitous SOD1 protein converts superoxide radical anions to oxygen and hydrogen peroxide. Patients with familial ALS caused by mutations in SOD1 can show comorbidity with frontotemporal dementia and develop cognitive impairment, including apathy, inattention, verbal deficits, and hypersexuality. At the cellular level, pathological signs of ALS may include tau immunoreactive astrocytic and neuronal inclusions, suggesting that cognitive dysfunction in ALS may also reflect abnormal protein metabolism of the microtubule associated protein (MAP), tau. To identify cell-specific expression changes, we performed laser capture microdissection (LCM) to isolate anterior horn motor neurons and surrounding cells. To determine common pathways for the development of ALS due to dysfunction of SOD1 or TAU, we performed whole transcriptome analysis in SOD1 and TAU mouse models. Because ALS is a neurodegenerative disease that specifically affects motor neurons, these cells were the main investigative target.  Global transcriptomes of glial cells surrounding the motor neurons were also assessed, because these cells have been implicated as triggers of neurodegeneration. Mouse experiments were performed at the presymptomatic stage, prior to the onset of cell loss, in order to reduce false positive signals due to tissue reactive changes. Lumbar anterior horn anterior horn motor neurons and surrounding cells (glia) were isolated from presymptomatic TAU-P301L and SOD1-G93A transgenic mice using laser capture microdissection (LCM; PixCell® IIe LCM System, Arcturus, Molecular Devices, CA). On average, 500 motor neuron bodies or surrounding glial cells from 20 tissue sections per animal were collected. RNA isolation from LCM collected cells was performed using the Qiagen RNeasy Micro Kit. Only RNA with RNA Integrity Numbers (RIN) above 7.5 were taken for further analysis (Agilent Bioanalyzer 2100). A two-round T7-based amplification and labeling protocol (Agilent Low RNA Input Linear Amplification Kit PLUS) was used to generate high quality labeled cRNA. Agilent Whole Mouse Genome Microarray comparisons of motor neurons and surrounding glia were performed between transgenic (SOD1G93A and TAUP301L) and corresponding nontransgenic (control) littermate animals, producing four independent comparison groups: SOD1G93A motor neurons versus control motor neurons (SOD1mn), SOD1G93A motor neuron surrounding glia versus control glia (SOD1gl), TAUP301L motor neurons versus control motor neurons (TAUmn) and TAUP301L glia versus control glia (TAUgl). Each comparison used four pairs of transgenic (SOD1G93A or TAUP301L) vs. corresponding control littermate animals, producing four biological replicates. Raw microarray data were acquired using the Agilent DNA Microarray scanner and processed with the accompanying Agilent Feature Extraction 10.5 Image Analysis software using default settings.  Normalized signal intensities were used to identify gene expression changes in SOD1G93A and TAUP301L motor neurons and surrounding glial cells, generating four partially overlapping sets of data. For the identification of differential expression, the genes were required to pass two conservative criteria: a ratio beyond the 99.5% confidence interval observed in homotypic comparisons, which corresponded to an approximately 1.5-fold expression change, and a paired t-test (P<0.01) computed using 100 permutations of the data for each gene. Correction for multiple comparisons was performed using the adjusted Bonferroni test.  The analysis was performed in the TM4: Microarray Software Suite. These techniques identified 251 transcripts representing 186 known genes for which expression was altered in at least one of the four comparisons.

overall_design: Four-condition experiment, SOD1G93A motor neurons versus control motor neurons (SODmn), SOD1G93A motor neuron surrounding glia versus control glia (SODgl), TAUP301L motor neurons versus control motor neurons (TAUmn) and TAUP301L glia versus control glia (TAUgl). Each comparison used four pairs of transgenic (SOD1G93A or TAUP301L) vs. corresponding control littermate animals, producing four biological replicates. Biological replicates: 4 SOD1G93A motor neurons (SODmn), 4 non SOD littermate motor neurons (nonSODmn), 4 SOD1G93A motor neuron surrounding glia (SODgl), 4 non SOD littermate motor neuron surrounding glia (nonSODgl), 4 TAUP301L motor neurons (TAUmn), 4 non TAU littermate motor neurons (nonTAUmn), 4 TAUP301L motor neuron surrounding glia (TAUgl), 4 non TAU littermate motor neuron surrounding glia (nonTAUgl). Four independent comparison groups were generated: SOD1G93A motor neurons versus control nonSOD motor neurons, SOD1G93A motor neuron surrounding glia versus control nonSOD glia, TAUP301L motor neurons versus control nonTAU motor neurons and TAUP301L glia versus control nonTAU glia. Each comparison used four pairs of transgenic (SOD1G93A or TAUP301L) vs. corresponding control littermate animals, producing four biological replicates. Each replicate was repeated twice with dye flip to correct for unequal dye incorporation rates. Therefore, eight microarray hybridizations were performed for each biological comparison, for a total of 32 microarray slides and generating four groups of differentially expressed genes in SOD1G93A motor neurons (SODmn), SOD1G93A motor neuron surrounding glial cells (SODgl), TAUP301L motor neurons (TAUmn), and TAUP301L surrounding glial cells (TAUgl).

first: Lili

last: Kudo


title: Analysis of natural wheat and spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

sample_organism:
Leuconostoc mesenteroides
Oenococcus oeni
Pediococcus acidilactici
Pediococcus pentosaceus
Staphylococcus aureus
Streptococcus thermophilus
Enterococcus faecalis
Enterococcus faecium
Enterococcus hirae
Lactococcus lactis
Lactobacillus acidophilus
Levilactobacillus brevis
Lentilactobacillus buchneri
Lacticaseibacillus casei
Weissella confusa
Lactobacillus delbrueckii
Lactobacillus helveticus
Lentilactobacillus hilgardii
Lactiplantibacillus pentosus
Lactiplantibacillus plantarum
Lactobacillus gasseri
Lacticaseibacillus paracasei
Limosilactobacillus reuteri
Latilactobacillus sakei
Companilactobacillus alimentarius
Lactobacillus amylovorus
Companilactobacillus farciminis
Limosilactobacillus fermentum
Fructilactobacillus fructivorans
Fructilactobacillus sanfranciscensis
Bifidobacterium
Brevibacterium linens
Latilactobacillus curvatus
Lactobacillus johnsonii
Leuconostoc citreum
Leuconostoc pseudomesenteroides
Limosilactobacillus pontis
Enterococcus casseliflavus
Mammaliicoccus lentus
Limosilactobacillus panis
Lacticaseibacillus rhamnosus
Lactobacillus crispatus
Enterococcus mundtii
Lactiplantibacillus paraplantarum
Companilactobacillus paralimentarius
Limosilactobacillus frumenti
Lentilactobacillus parabuchneri
Companilactobacillus mindensis
Furfurilactobacillus rossiae


title: Mycobacterium tuberculosis Complex Clinical Isolates exhibit unique gene expression profiles in vitro and inside macrophages

status: Public on Jul 09 2010

city: Ithaca

first: David

last: Russell

state: NY

address: C5 171 Veterinary Medical Center

department: College of Veterinary Medicine

institute: Cornell University

first: D


title: Identification and validation of causal genes for atherosclerosis in mice

status: Public on Jun 23 2010

city: Seattle

first: Xia

last: Yang

address: 1100 Fairview Ave N

institute: Sage Bionetworks

summary:
Identification of causal genes for atherosclerosis in a segregating mouse population and validation via single-gene knockout and plaque progression mouse models.

This SuperSeries is composed of the SubSeries listed below.


title: NP-18 vs. NP-18AR transcriptional profile upon treatment with TK/GCV

status: Public on Jul 16 2010

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary: Pancreatic cancer-derived cells NP-18 underwent four rounds of treatment with increasing doses of an adenoviral vector encoding TK enzyme and GCV. Surviving cells were termed NP-18AR and displayed decreased sensitivity to treatment. This experiment analyses the transcriptomic effect of TK/GCV treatment on NP-18AR as compared to that of NP-18 cells.

overall_design: Two-condition experiment, where response  to treatment in naïve cells (NP-18) was compared to response to treatment in previously treated resistant cells (NP-18AR). Biological replicates: samples from 3 independently generated and independently treated NP-18AR lines (NP-18AR1, NP-18AR2 and NP-18AR3) were hibridized with 3 independently treated samples of NP-18 cells. A total of 9 hybridizations were performed, 2 for NP-18AR1 (including 1 dye-swap), 4 for NP-18AR2 (including 2 dye swaps) and 3 for NP-18AR3 (including 1 dye-swap).

first: Daniel

last: Abate-Daga

first: Cristina

last: Fillat


title: Genetic Copy Number Variants in Sib Pairs Both Affected with Schizophrenia

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

institute: Taiwan National Health Research Institute

summary: Genome-wide screening for DNA copy-number variations (CNVs) was conducted for ten pairs, a total of 20 cases, of affected siblings using oligonucleotide array-based CGH. We found negative symptoms were significantly more severe (p < 0.05) in the subgroup that harboring more genetic imbalance (n ≧ 13, n = number of CNV-disrupted genes) as compared with the subgroup with fewer CNVs (n ≦ 6), indicating the degree of genetic imbalance may influence the severity of schizophrenia negative symptoms. Four central nervous system (CNS) related genes including CCAAT/enhancer binding protein, delta (CEBPD, 8q11.21), retinoid X receptor, alpha (RXRA, 9q34.2), LIM homeobox protein 5 (LHX5, 12q24.13) and serine/threonine kinase 11 (STK11, 19p13.3) are recurrently (incidence ≧16.7%) disrupted by CNVs. Two genes, PVR (poliovirus receptor) and BU678720, are concordant deleted in one and two, respectively, pairs of co-affected siblings. However, we did not find significant association of this BU678720 and schizophrenia in a large case-control sample. We conclude that the high genetic loading of CNVs may as the underlying cause of schizophrenia negative symptoms, and the CNS-related genes revealed by this study warrants further investigation.

overall_design: Ten pairs, a total of 20 cases, of schizophrenia affected siblings were analyzed. The reference genomic DNA pools used for this study were constructed by pooling equal amounts of DNA extracted from ten healthy men or ten healthy women who live in Taiwan. Each array hybridization experiment was performed with differentially labeled gender-matched samples, one from the affected individual, and the other from the DNA control pool. To rule out probable CNPs in our ethnic group, two array hybridization experiments were performed using the male or female pooled control and the same-gender commercialized normal Caucasian samples (Promega, Madison, WI, USA).

first: C

middle: H

last: Liu

first: H

middle: G

last: Hwu


title: Identification of differentially expressed genes in early inner ear development

status: Public on Jun 21 2010

city: Salt Lake City

first: Christian

middle: N.

last: Paxton

state: UT

department: Neurobiology and Anatomy

institute: Christian

summary: The first morphological evidence of the developing ear is a thickened disk of ectoderm known as the otic placode. However, signals for otogenesis are present even before the otic placode is physically apparent. Several inductive signals have been identified through candidate gene approaches, but there are still many gaps in the signaling cascade of otogenesis. Presently the candidate gene approach has largely exhausted known candidates. This project compares the pre-otic domain with a control region that is competent, but not specified to form otic placode. The purpose of this work is to identify genes that are differentially expressed in the pre-otic domain in order to generate a list of novel candidate genes for otic placode induction.

overall_design: Two condition experiment, pre-otic domain vs. rostral control (competent but not specificied to form otic placode); Biological replicates: 4 replicates for each condition consisting of pooled samples from 7 bi-lateral tissue microdissection; dye swap

middle: N

first: Steven

middle: B

last: Bleyll

first: Susan

middle: C

last: Chapman

first: Gary

last: Schoenwolf


title: HER-2 signaling, acquisition of growth factor independence, and regulation of biological networks associated with cell transformation

status: Public on Aug 24 2010

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R, HWCRC rm 815

institute: Karmanos Cancer Inst., Wayne State University


title: The function of OsCERK1 in the chitin elicitor signaling in Rice

city: Kawasaki

first: Hanae

last: Kaku

state: Kanagawa

address: 1-1-1, Higashi-Mita, Tama-ku

department: Life Sciences

institute: Meiji University

summary:
To see the function of OsCERK1 receptor-like kinase in the chitin elicitor signaling in Rice, we compared the gene expression profiles in the chitin oligosaccharide treated cultured rice cells of vector control and OsCERK1 knock-down mutant (RNAi).
Keywords: Defense response

overall_design: 1,Chitin oligosaccharide treatment (vector control), 2,Chitin oligosaccharide treatment (vector control) color swap, 3,Chitin oligosaccharide treatment (OsCERK1 RNAi), 4,Chitin oligosaccharide treatment (OsCERK1 RNAi) color swap

first: Yoshitake

last: Desaki

first: Takuto

last: Nakano


title: Resistance to TFT by decreased TK or overexpression of sPLA2

status: Public on Jun 15 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: Trifluorothymidine (TFT) is part of the novel oral formulation TAS-102, which is currently evaluated in phase II studies. Drug resistance is an important limitation of cancer therapy. The aim of the present study was to induce resistance in the colon cancer cell line H630 using two different exposure schedules and to analyze the resistance mechanism. Cells were exposed either continuously or intermittently to TFT, resulting in H630-cTFT and H630-4TFT, respectively. Cells were analyzed for cross resistance, cell cycle, protein expression and activity of thymidine phosphorylase (TP), thymidine kinase (TK) and thymidylate synthase (TS), gene expression (microarray) and genomic alterations (array CGH). Both cell lines were cross-resistant to 2’-deoxy-5-fluorouridine (>170-fold). Exposure to IC75-TFT increased the S- and G2/M-phase of H630 cells, while in the resistant variants no change was observed. The two main target enzymes TS and TP remained unchanged in both TFT-resistant variants. In H630-4TFT cells, TK protein expression and activity were decreased, possibly related to an aberrant TK protein, clearly resulting in less activated TFT and most likely the mechanism of TFT resistance. Surprisingly, in H630-cTFT microarray analysis revealed a strong increase in mRNA levels of secretory phospholipase-A2 (sPLA2; 47-fold), which was also found by RT-PCR (211 fold increase). Inhibition of sPLA2 reversed TFT resistance partially. In addition, H630-cTFT had many chromosomal aberrations, but the exact role of sPLA2 in TFT-resistance remains unclear. Altogether, induction of resistance to TFT can lead to different mechanisms of resistance, including decreased TK protein expression and enzyme activity, as well as (phospho)lipid metabolism.

overall_design:
In the present in vitro study, we aimed to characterize whether different protocols to induce resistance to TFT would also result in various types of resistance genotypes and phenotypes. Induction of resistance was either performed by (1) classical continuous exposure to increasing low concentrations of TFT, or (2) by intermittent short exposure to high TFT concentrations every week, which is in general a more clinically relevant schedule. The TFT resistant H630 variants were characterized by comparative genome hybridization (CGH)-analysis and expression analysis to gain a more in depth insight in the mechanisms underlying TFT resistance.

The following supplementary files contain raw data for Samples GSM452725, GSM452756, and GSM453572:
GSE18137_MAF_251495016981_S01_CGH_v4_95_Feb07_1_1.txt
GSE18137_MAF_251495016981_S01_CGH_v4_95_Feb07_1_3.txt

last: Temmink

last: Bijnsdorp

last: Prins

first: N.

last: Losekoot

last: Adema

first: K.

last: Smid

last: Honeywell

first: B.

last: Ylstra

last: Eijk

first: M.

last: Fukushima

last: Peters


title: Characterization of sensor-specific stress response by transcriptional profiling of wsc1 and mid2 deletion strains and chimeric sensors in Saccharomyces cerevisiae

status: Public on Jun 19 2010

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

institute: Facultad de Farmacia (UCM)


title: Comparison of retinal gene expression in wild-type and XOPS-mCFP (rod degeneration) transgenic zebrafish

status: Public on Jun 09 2010

city: Lexington

first: Ann

middle: Caroline

last: Morris

state: KY

address: 215 T.H. Morgan Building

department: Department of Biology

institute: University of Kentucky

summary: Purpose. XOPS-mCFP transgenic zebrafish experience a continual cycle of rod photoreceptor development and degeneration throughout life, making them a useful model to investigate the molecular determinants of rod photoreceptor regeneration. The purpose of this study was to compare the gene expression profiles of wild type and XOPS-mCFP retinas in order to identify genes that may contribute to the regeneration of the rods.   Methods. Wild type and XOPS-mCFP retinal mRNA was subjected to microarray analysis using the Agilent platform. The Ingenuity Pathway Analysis program was used to identify biologically relevant processes that were significantly represented in the dataset. Expression changes were verified by RT-PCR. Selected genes were further examined during retinal development and in adult retinas by in situ hybridization, immunohistochemistry, and using a transgenic fluorescent reporter line.   Results. Over 600 genes displayed significant expression changes in XOPS-mCFP retinas compared to wild type controls. Many of the downregulated genes were associated with phototransduction, whereas upregulated genes were associated with several biological functions, including cell cycle, DNA replication and repair, cell development and cell death. RT-PCR analysis of a subset of these genes confirmed the microarray results. Three transcription factors (sox11b, insm1a, and c-myb) displaying increased expression in XOPS-mCFP retinas were also expressed throughout retinal development and in the persistently neurogenic ciliary marginal zone.   Conclusions. This study identified numerous gene expression changes in response to rod degeneration in zebrafish, and further suggests a role for the transcriptional regulators sox11b, insm1a, and c-myb in both retinal development and rod photoreceptor regeneration.

overall_design: Two-condition experiment: wild-type vs. XOPS-mCFP retinas. Four biological replicates for each condition. RNA was prepared from one retina for each sample. Each hybridization was accompanied by a dye-swap control, for a total of eight array hybridizations.

first: Marie

last: Forbes-Osborne

first: Lakshmi

last: Pillai

first: James

last: Fadool


title: Global analysis of DNA methylation patterns and different histone modification patterns on the latent KSHV episome

status: Public on Jun 07 2010

city: Hamburg

first: Thomas

last: Guenther

department: Mechanisms of Antiviral Defense

institute: Heinrich-Pette-Institut

type: Methylation profiling by genome tiling array


title: Actions and interactions of progesterone and estrogen on transcriptome profiles of the bovine endometrium

status: Public on Sep 30 2010

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary:
By comparison of the transcriptome profiles of infected and healthy udder tissue we analyse gene expression in the late stage of infection with E. coli 1303.
Differentially expressed genes and transcription factors regulating coexpressed genes identified by SOTA clustering were used to identify key genes that define late stage of infection with E. coli 1303.

Keywords: hormone treatment

overall_design: 12 samples, four conditions: bovine endometrium of ovariectomized cows treated w/wo steroid hormones  * three replicates

first: T

last: Shimizu

first: S

first: H

last: Blum

first: E

last: Wolf

first: A

last: Miyamoto


title: SuperSeries for the study of expression pattern analysis of Thermus thermophilus HB8

status: Public on Oct 15 2010

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute


title: Acute Molecular Response of Mouse Hindlimb Muscle To Chronic Stimulation

status: Public on Jun 01 2010

city: Pittsburgh

first: John

middle: Michael

last: Krill-Burger

state: PA

address: Rm. WG21.3 Shadyside Hospital

institute: University of Pittsburgh Medical Center

summary:
Stimulation of the mouse hindlimb via the sciatic nerve was used to induce contractions for 4 hours to investigate acute muscle gene activation in a model of muscle phenotype conversion. Initial force production (1.6 + 0.1 g/g body weight) declined 45% within 10 min and was maintained for the remainder of the experiment. Force returned to initial levels upon completion of the study.  An immediate-early growth response was present in the EDL (FOS, JUN, ATF3, MAFK) with a similar but attenuated pattern in the soleus.  Transcript profiles showed decreased fast fiber specific mRNA (myosin heavy chains 2A, 2B; troponins T3, I; alpha-tropomyosin, m-creatine kinase) and increased slow transcripts (myosin heavy chain slow/1beta, troponin C, tropomyosin 3gamma) in the EDL.  Histological analysis of the EDL revealed glycogen depletion without inflammatory cell infiltration or myofiber damage in stimulated vs. control muscles. Several fiber type specific transcription factors (EYA1, TEAD1, NFATc1 and c4, PPARG, PPARGC1alpha and beta, BHLHB2) increased in the EDL along with transcription factors characteristic of embryogenesis (KLF4, SOX17, TCF15, PKNOX1, ELAV). No established in vivo satellite cell markers or the genes activated during our parallel studies of satellite cell proliferation in vitro (CYCLINS A2, B2, C, E1, MyoD) increased in the stimulated muscles. These data indicated that onset of fast to slow phenotype conversion occurred in the EDL within 4 hours of stimulation without satellite cell recruitment or muscle injury but was driven by phenotype specific transcription factors from resident fiber myonuclei including activation of nascent developmental transcriptional programs.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Response of bovine mammary tissue to experimental Staphylococcus aureus infection

status: Public on May 20 2010

city: St Lucia

first: Ylva

last: Strandberg-Lutzow

state: Queensland

address: 306 Carmody Road

department: Livestock Industries

country: Australia

institute: CSIRO

summary:
Mastitis in dairy cattle can result from infection by a range of microorganisms but is principally caused by coliform bacteria and gram positive bacteria such as Staphylococcus aureus (S. aureus). The former species are often acquired by environmental contamination while S. aureus is particularly problematic due to its resistance to antibiotic treatments and ability to reside within mammary tissue in a chronic, subclinical state. The transcriptional and translational responses within bovine mammary epithelial tissue subjected to intramammary challenge with S. aureus are poorly characterised, particularly at the earliest stages of infection. A Bovine Innate Immune Microarray was employed to measure changes in gene expression occurring in bovine mammary tissues sampled from three dairy cows after a brief and graded intramammary challenge with a virulent strain of S. aureus.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Animal infected with vaying doses of S. aureus in different udder locations were compared to a single control uninfected tissue and to the other 2 locations at each infective dose. Dye swaps were performed for each comparison.