title: Gene Expression Profiling of Fixed Tissues of Lymph Node Metastasis in Hepatocellular Carcinoma

city: Shanghai

first: Zuolin

last: Xiang

address: 136 Yi Xue Yuan Road

institute: Zhongshan Hospital, Fudan University

summary: RNA was extracted from formalin-fixed specimens of paired intratumoral and peritumoral tissues of patients with lymph node-positive (n=20) or negative (n=20) HCC. A cDNA-mediated annealing, selection, extension, and ligation assay was performed with an array of 502 known cancer-related genes to identify differentially expressed genes in 80 RNA samples.

overall_design: Total RNA was purified from the tissue specimens using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. DASL experiments were performed to identify genes that were differentially expressed between the lymph node metastasis (LNM) and non-lymph node metastasis (NLNM) groups of matched intratumoral and peritumoral tissues by using A cDNA-mediated annealing, selection, extension, and ligation assay.

first: Zuo-Lin

first: Zhao-Chong

last: Zeng

first: Jia

last: Fan

first: Zhao-You

last: Tang

first: Hai-Ying

first: Dong-Mei

last: Gao


title: Gene expression analysis using the ureters of normal and ureteritis mice

status: Public on Aug 02 2011

city: Sapporo

first: Osamu

last: Ichii

state: Hokkaido

address: Kita 18-Nishi 9

department: Faculty of Veterinary Medicine

country: Japan

institute: Hokkaido University

summary: Analysis of ureters of idiopathic ureteritis mice. The B cell functions associated genes were upregulated in the diseased ureters compared to nomal ureter. These results provide a basical information of molecular pathology in idiopathic ureteritis.

overall_design: In the study, the normal ureter (n=3) and diseased ureter (n=3) were used. The total RNA sample of each group was collected to 1 sample, 36,142 genes expressions were compared between these groups.


title: Identification of differentially expressed genes in matched primary and metastatic melanoma tumor pairs

city: Leeds

first: Rosalyn

last: Jewell

address: Leeds Cancer Research UK Centre, LIMM, Cancer Genetics Building, St James;s University Hospital, Beckett Street

department: Section of Epidemiology and Biostatistics

country: United Kingdom

institute: University of Leeds

summary: Comparison of gene expression profiles between a primary melanoma and an early metastatic specimen from the same patient will provide essential biological insight into early metastatic processes. The DASL (cDNA mediated annealing, selection, extension and ligation) assay has been used to generate gene expression data for 502 cancer-related genes from very small formalin-fixed sentinel node biopsy (SNB) melanoma samples, this data has been further compared with gene expression of the matched formalin-fixed primary melanoma. Tissue was sampled from twenty-five SNB deposits using laser capture microdissection. The mean number of genes detected using DASL with SNB samples was lower than when using a core of primary melanoma tumor (242 versus 434 genes). A large proportion of SNB samples failed (<240 genes detected) the assay (57.7%). Area of tissue microdissected, RNA concentration and qRT-PCR quality control did not predict performance of samples on the array but age of sampled tissue negatively correlated with number of genes detected (p=0.01). For samples that performed successfully, matched primary samples were available for 10 samples. Gene expression profiles correlated between all matched tumor pairs (Spearman’s rho 0.15-0.80, p<0.01), although a number of genes were differentially expressed between nodal and primary tumors in all tumor pairs. This study demonstrates that the DASL assay can be used to generate gene expression data from small formalin-fixed samples, but not consistently. Differentially expressed genes were identified across 10 matched primary and nodal tumor pairs suggesting that the DASL assay could be used to derive essential biological information about early metastasis.

overall_design: Formalin-fixed paraffin-embedded SNB samples and primary tumors were identified from two study sets. In Study 1, population ascertained melanoma patients were recruited to a cohort in the period from 2000 till the present day. Eight positive SNB samples were identified, from patients whose primary tumors had already been sampled for DASL studies. In Study 2, seventeen positive SNB samples were identified in a study designed to identify predictors of sentinel node positivity and relapse (SNB study). One nodal RNA sample, microdissected from a diagnostic H&E slide, was not sent for DASL analysis because of low RNA concentration (0.37 ng/μl), therefore a total of 26 nodal samples (including 2 replicate samples) were supplied to the Illumina DASL service provider. Of the 11 samples successfully yielding gene expression data, 10 had matched primary samples (e.g., Node_1 and Primary_1) for which gene expression data were available and is presented in this data set.

middle: A


title: Great Ape Copy Number Variation

status: Public on Aug 03 2011

city: Barcelona

first: Arcadi

last: Navarro

address: Plaça Charles Darwin, 1

country: Spain

institute: University Pompeu Fabra

type: Genome variation profiling by genome tiling array

summary: Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases.

sample_organism:
Gorilla gorilla
Gorilla gorilla gorilla
Pan paniscus
Pan troglodytes
Pongo pygmaeus
Pongo abelii
Pongo sp.
Pan troglodytes troglodytes

overall_design: Each sample is hybridized against a common reference of the same species for two dye combinations (e.g. chimp1_CY5 vs chimpREF_Cy3; chimp1_CY3 vs chimpREF_Cy5; bonobo1_CY5 vs bonoboREF_Cy3; bonobo1_CY3 vs bonoboREF_Cy5;)

first: Elodie

last: Gazave

first: Fleur

last: Darré

first: Carlos

last: Morcillo-Suarez

first: Natalia

last: Petit-Marty

first: Angel

last: Carreño

first: Urko

middle: M

last: Marigorta

first: Oliver

last: Ryder

first: Antoine

last: Blancher

first: Mariano

last: Rocchi

first: Elena

last: Bosch

first: Carl

last: Baker

first: Tomàs

last: Marquès-Bonet

first: Evan

middle: E

last: Eichler


title: Affymetrix SNP array data for mammary tumors that recurred after inactivation of the oncogenic PIK3CA-H1047R

city: boston

first: jean

last: zhao

address: 450 Brookline Ave

department: cancer biology

country: USA

institute: dana-farber cancer institute

summary: Gain-of-function mutation of PIK3CA represents one of the most common oncogenic events in human malignancy, making PI3K an attractive target for cancer therapy. Despite the great promise of targeted therapy, drug resistance is likely to develop, causing treatment failure. To elucidate resistance mechanisms to PI3K-targeted therapy, we constructed a mouse model of breast cancer conditionally expressing PIK3CA-H1047R. Surprisingly, the majority of mammary tumors induced by PIK3CA-H1047R expression recurred following PIK3CA-H1047R inactivation. Genomic analyses of recurrent tumors revealed multiple lesions, including spontaneous focal amplification of c-Met or c-Myc. While amplification of c-Met allowed tumor survival dependent on activation of endogenous PI3K, tumors with amplification of c-Myc become independent of the PI3K pathway. Functional analyses further demonstrated that c-Myc contributed to tumors’ independence of oncogene and resistance to PI3K inhibition. Together, our data suggest that MYC elevation in tumors may be a potential mechanism conferring resistance to current PI3K-targeted therapies.

overall_design: Affymetrix SNP array analysis was performed with Mouse Diversity Genotyping Arrays (Affymetrix) on genomic DNA extracted from frozen biopsies of 6 recurrent mouse mammary tumor samples. Copy number analysis was performed for the mouse mammary tumors using genomic DNA from normal mammary tissue as the reference for copy number inference.

first: Hailing

last: Cheng

first: Pixu

last: Liu

first: Jean

last: Zhao


title: Structural genomic variation among soybean NIL's using CGH approach

city: Saint Paul

first: Robert

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

summary: CGH was used to map structural variation (introgressed regions) among soybean iron-inefficient NIL IsoClark with its iron-efficient recurrent parent Clark and donor parent T203. Another NIL series HiPro, LoPro was also used in the study.

overall_design: CGH Comparisions were made among a NIL IsoClark with its parents Clark and T203; also comparisions were made among HiPro and LoPro NIL series. The soybean tiling array consists of 700k probes, spaced at approximately 1.1 kb intervals.

first: Pudota

middle: B

last: Bhaskar

first: William

middle: J

last: Haun


title: Evaluation of the role of functional constraints on the integrity of an ultra conserved region in the genus Drosophila

city: Wuhan

first: Xiao-Qin

last: Xia

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

department: Center for Molelcular and Cellular Biology of Aquatic Organisms

country: China

institute: Institute of Hydrobiology, the Chinese Academy of Sciences

summary: Our results indicate that even in highly rearranged genomes like those of Diptera, unusually high levels of gene order conservation cannot be systematically attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought.

overall_design: 6 genotypes (REC, INV1, INV2, SIM1, REV1, and REV2) and 2 sexes (male and female) were investigated in this study, each with 3 biological replicates (A,B,and C), so a total of 36 (6x2x3) hybridizations were conducted. Differential analysis between genotypes or sexes were analyzed.

first: Carlos

last: Díaz-Castillo

first: José

last: Ranz


title: Fundulus exposed to arsenic as embryos

status: Public on Aug 01 2011

city: Pendleton

first: Lisa

last: Bain

state: SC

address: P. O. Box 709

department: Biological Sciences

institute: Clemson University

summary: The present study used microarray expression profiling to determine the effects of embryonic arsenic exposure.  Fertilized killifish (Fundulus heteroclitus) eggs were exposed to 0, 5, 15, or 25ppm arsenic as sodium arsenite.  To examine differentially expressed genes, the microarrays were probed using RNA obtained from the control and 25ppm-exposed killifish just after hatching.  No differences were noted in survival or hatching success between any of the groups.  After analysis, a set of 332 genes was found to accurately distinguish between the control and 25ppm exposure groups.  Expression of several of the genes (CDBP1, Arts1, FetB, and Fbp7) was quantified by qPCR in the lower exposure groups and at earlier time points to examine temporal and dose-responsive expression patterns.  These results will enable us to better understand how arsenic impacts development.

overall_design: Killifish eggs were fertilized, divided into petri dishes containing 40 eggs (n=10 replicate petri dishes), and cultured until hatch in 0 or 25 ppm arsenic as sodium arsenite.  Four to five hatchlings within each petri dish were pooled to obtain RNA.  A total of 20 arrays were probed, 10 with RNA from control fish and 10 with RNA from the arsenic-exposed fish.

first: Kristen

last: Gaworecki

middle: W

last: Chapman

first: Marion

last: Beal


title: Radiation-Induced Genomic Instability in Caenorhabditis Elegans

city: Kuopio

first: Katriina

last: Huumonen

address: PO. Box 1627

department: Department of Environmental Sciences

country: Finland

institute: University of Eastern Finland

summary: Significant impacts on gene expression were observed generations after exposure in ionising radiation exposed nematodes.

overall_design: C. elegans were exposed to 1 Gy of X-rays and their gene expression was analysed several generations later with whole genome oligoarrays (Washington University).

first: Merja

last: Korkalainen

first: Hanna-Kaisa

last: Immonen

first: Matti

last: Viluksela

first: Mikko

last: Hiltunen

first: Keith

last: Baverstock

first: Juha

last: Parviainen

first: Tapani

last: Lahtinen

first: Garry

last: Wong

first: Jonne

last: Naarala

first: Jukka

last: Juutilainen


title: Rhabdomyosarcomas in aging A/J mice

city: Bar Harbor

first: Roger

last: Sher

address: 600 Main Street

institute: The Jackson Laboratory

summary: Rhabdomyosarcomas (RSCs) are skeletal muscle neoplasms found in humans and domestic mammals. The A/J inbred strain developed a high frequency of RSC by 20 months of age while BALB/cJ and BALB/cByJ also develop RSC but less frequently. These neoplasms affected skeletal muscle surrounding either the axial or proximal appendicular skeleton and were characterized by pleomorphic cells with abundant eosinophilic cytoplasm, multiple nuclei, and cross striations that invaded locally. The diagnosis was confirmed by detection of alpha-sarcomeric actin and myogenin in the neoplastic cells using immunocytochemistry. The A/J strain, but not the related BALB/c substrains, is also characterised by a progressive muscular dystrophy homologous to limb-girdle muscular dystrophy type 2B. The association between the development of RSC in similar muscle groups to those most severely affected by the progressive muscular dystrophy suggested that these neoplasms developed from abnormal regeneration of the skeletal muscle exacerbated by the dysferlin mutation. Transcriptome analyses revealed marked downregulation of genes in muscular development and function signaling networks. Non-synonymous coding SNPs were found in Myl1, Abra, Sgca, Ttn, and Kcnj12 suggesting these may be important in the pathogenesis of RSC. These studies suggest that A strains of mice can be useful models for dissecting the molecular genetic basis for development, progression, and ultimately for testing novel anticancer therapeutic agents dealing with rhabdomyosarcoma.

overall_design: Total RNA obtained from skeletal muscle samples from neoplastic and non-neoplastic tissues. Four rhabdomyosarcomas (~450 day old male A/J mice) and 8 nonneoplastic skeletal muscle samples (425-550 day old male A/J mice) were used

first: Gregory

last: Cox

first: Kevin

middle: D

last: Mills

first: John

middle: P

last: Sundberg


title: Molecular mechanism of DNA minor groove binding ligand as a radiation modulator

city: Delhi

first: Vibha

last: Tandon

state: Delhi

address: Department of Chemistry

department: Department of Chemistry

country: India

institute: University of Delhi

summary: Radiation-induced DNA damage initiates a complex series of overlapping responses responsible for the maintenance of genome integrity. This study reports the expression analysis in response to DNA minor groove binding ligand (DMA-5-(4-methylpiperazin-1-yl)-2-[2’-(3,4-dimethoxyphenyl)-5`-benzimidazolyl] benzimidazole, an analogue of Hoechst 33342), with an emphasis on its ability to afford better protection in cells exposed to ionizing radiation.

overall_design: Four different types of samples were employed in the analysis: Control (untreated) cells, 50µM ligand-treated cells, 2Gy radiation-treated cells, and cells treated with 50µM ligand one hour prior to 2Gy irradiation.

first: Atul

last: Ranjan


title: Comparative genomic hybridization study of Streptococcus pneumoniae

city: Rockville

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

summary:
PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships.

The Pneumococcus are among most deadly pathogens world-wide. The infections and outbreaks caused by this pathogens is quite frequent despite existing diagnostic network and therapeutic means. Therefore, developing reliable diagnostic tools and efficient (broad-spectrum) therapeutics for  Streptococcus pneumoniae remain a public health priority for every country in world today.

The comparative genomics study will provide the largest hitherto genomic data sets regarding this pathogen.These large data sets will enable us as well as other members of scientific community to conduct comprehensive data mining in the form of gene association studies with statistical power and significance.

sample_organism:
Streptococcus oralis
Streptococcus pneumoniae
Streptococcus mitis
Streptococcus infantis
Streptococcus pneumoniae TIGR4
Streptococcus pseudopneumoniae
Streptococcus oralis SK255

overall_design: Two hundread fifty five query strains were investigated in this study, with each query strain hybridized against the reference strain, tigr4.  Each strain has a single dye experiment.  Each oligo is spotted on the S.pneumoniae species microarray once.  Positive controls on the array consist of oligos designed from the sequenced reference genome of S. pneumoniae and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.

first: Leka

last: Papazisi

first: Eric

middle: C

last: Snesrud

first: Pratap

last: Venepally

first: Sarah

last: Akkoush

first: Adrian

last: Pineda

first: Erik

last: Wester

first: M

last: Kim

first: Lakshmi

last: Viswanathan

first: Dana

last: Busam

first: Jia

last: Liu

first: Alex

last: Saeed

first: Malene

last: Bek-Thompson

first: Bernard

last: Beal

first: Mogens

last: Killian

first: Tatiana

last: Dracheva

first: Robert

last: Fleischmann

first: Scott

middle: N

last: Peterson


title: miRNA profiling of 36 cases of diffuse large B cell lymphoma

city: Madrid

first: Santiago

last: Montes-Moreno

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Pathology

institute: CNIO

summary: miRNA expression data from 36 cases of RCHOP treated DLBCL samples were correlated with clinical variables in order to find miRNA signatures related with outcome.

overall_design: Cases classified according to the cell of origin classsifer (Wright G, Tan B, Rosenwald A, Hurt EH, Wiestner A, Staudt LM. A gene expression-based method to diagnose clinically distinct subgroups of diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2003;100:9991-6.) based on gene expression were subjected to miRNA expression profiling.

first: S

last: Montes Moreno

first: N

last: Martinez


title: Coupled evolution of transcription and mRNA degradation.

city: Rehovot

first: Itay

last: Tirosh

address: herzl

department: Molecular genetics

country: Israel

institute: Weizmann Institute of Science

summary: We measured mRNA levels of two yeast species (S.cerevisiae and S.paradoxus) and their hybrid, at four time-points (0, 20min, 40min, 60min) following transcription arrest using 1,10-Phenantroline (150ug/ml). This data was used to infer mRNA degradation rates of orthologous genes, study the divergence of mRNA degradation rates and the contribution of cis and trans mutations.

sample_organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

platform_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

overall_design: For each of the two biological repeats and each of the four time point, poly(A) mRNAs of the two species was pooled and labeled with cy3 while hybrid poly(A) mRNA was labeled with cy5 and these were hybridized to our custom two-species microarray (Agilent) with four subarrays.


title: Growth phase-associated changes in Lactobacillus rhamnosus GG

city: Helsinki

first: Kati

last: Laakso

address: Meijeritie 4

department: R&D

institute: Valio Ltd

summary:
Transcriptional profiling of probiotic Lactobacillus rhamnosus GG during growth in industrial-type whey medium in pH-controlled bioreactor cultures at two different growth pH: 4.8 and 5.8.
Keywords: growth phase, growth pH

overall_design: Cell samples from three biological replicates were harvested at mid-exponential (4 h), late exponential (12 h), stationary transition point (16 h), early stationary (20 h) and late stationary (31 h) phases, all these samples both from pH 4.8 and 5.8 cultivations. A total of 66 hybridizations were performed according to ANOVA design where all possible direct pair-wise comparisons within biological replicates were conducted. Growth series between treatments (pH 4.8 or pH 5.8) were combined together by hybridizing RNA samples from the treatments at time points 12 h and 31 h to microarrays using dye-swap replicates. Treatments were paired twice and each biological replicate was used only once to form the pairs. Other comparisons between the two pH treatments were estimated computationally.

first: Kerttu

last: Koskenniemi

first: Johanna

last: Koponen

first: Matti

last: Kankainen

first: Anu

last: Surakka

first: Tuomas

last: Salusjärvi

first: Petri

last: Auvinen

first: Kirsi

last: Savijoki

first: Tuula

last: Nyman

first: Nisse

last: Kalkkinen

first: Soile

last: Tynkkynen

first: Pekka

last: Varmanen


title: Expression profile of Maize (Zea mays L.) Embryonic Axes During Germination: Regulation of Ribosomal Protein mRNAs.

city: Mexico City

first: Laura

middle: I

last: Uribe

state: DF

address: Periferico Sur 4124 Col. Ex rancho de Anzaldo

department: Research

country: Mexico

institute: INMEGEN

summary:
Seed germination is a critical developmental process in plant propagation. Knowledge of the gene expression patterns  in this critical process  is important in order to  understand the main biochemical reactions involved in successful germination, specially for economically relevant plants such as Maize.
The purpose of this study is the gene expression analysis of quiescent and germinated maize embryonic axes to determine the regulatory mechanism for (r)-protein expression during the maize development process.

overall_design: This study analyzed samples of total and polysomal RNA from maize embryonic axes at different time periods during the germination process and under the influence of a specific growth factor. For each condition a biological replicate was included and for the time periods, a technical replicate was also included.

first: Sara

last: Jimenez-Lòpez

first: Eder

last: Mancera-Martinez

first: Alberto

last: Donayre-Torres

first: Claudia

last: Rangel-Escareño

last: Uribe-Figueroa

last: March-Mifsut

first: Gerardo

last: Jimenez-Sanchez

first: Estela

last: Sanchez de Jimenez


title: Differential gene expression in resistant and susceptible peanut cultivars during Aspergillus infection

first: Natalie

last: Fedorova

department: Infectious Disease

institute: JCVI

summary: To identify peanut Aspergillus-interactive and Aspergillus-resistance genes, we carried out a large scale peanut Expressed Sequence Tag (EST) project followed by a peanut microarray study.  For expression profiling, resistant and susceptible peanut cultivars were infected with a mixture of Aspergillus flavus and parasiticus spores.  Microarray analysis identified 65 and 1 genes in resistant (C20) and susceptible (TF) cultivars, respectively, that were up-regulated in response to Aspergillus infection. In addition we identified 40 putative Aspergillus-resistance genes that were constitutively up-expressed in the resistant cultivar in comparison to the susceptible cultivar. Some of these genes were homologous to peanut, corn, and soybean genes previously shown to confer resistance to fungal infection.  These results provide a comprehensive genome-scale platform for future studies focused on developing Aspergillus-resistant peanut cultivars through conventional breeding, marker-assisted breeding, or biotechnological methods by gene manipulation.

overall_design:
Four samples were analyzed with four hybs. Two samples were obtained from
resistant (C20) and  and susceptible (TF) cultivars. Two factors were varied in the experimental design: (i) peanut
cultivars (resistant (GT-C20) and susceptible (TF)) and (ii) Aspergillus exposure. A combination of these factors
produced four hybridizations as follows:
(1) C20Y vs. TFY (GT-C20 infected vs. TF infected)
(2) C20Y vs. C20N (GT-C20 infected vs. not infected)
(3) TFY vs. TFN (TF infected vs. not infected)
(4) C20N vs. TFN (GT-C20 not infected vs. TF not infected)

first: Baozhu

last: Guo

first: Xiaoping

last: Chen

first: Chun-Hua

last: Wan

first: William

last: Nierman

first: Deepak

last: Bhatnagar

first: Jiujiang

last: Yu


title: Transcript profiles of PFAAs in trout liver

city: Logan

first: Abby

last: Benninghoff

state: UT

address: 4815 Old Main Hill

department: Animal, Dairy and Veterinary Sciences

institute: Utah State University

summary: Background: Previously, we reported that perfluorooctanoic acid (PFOA) promotes liver cancer in manner similar to that of 17β-estradiol (E2) in rainbow trout. Also, other perfluoroalkyl acids (PFAAs) are weakly estrogenic in trout and bind the trout liver estrogen receptor (ER). Objectives: The primary objective of this study was to determine whether multiple PFAAs enhance hepatic tumorigenesis in trout, an animal model that represents human insensitivity to peroxisome proliferators. Methods: A two-stage chemical carcinogenesis model was employed in trout to evaluate PFOA, perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), perfluorooctane sulfonate (PFOS) and 8:2 fluorotelomer alcohol (8:2FtOH) as complete carcinogens or promoters of aflatoxin B1 (AFB1)- and/or N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced liver cancer. A custom trout DNA microarray was used to assess hepatic transcriptional response to these dietary treatments in comparison to E2 and the classic peroxisome proliferator clofibrate (CLOF).  Results: Incidence, multiplicity and size of liver tumors in trout fed diets containing E2, PFOA, PFNA and PFDA were significantly higher compared to AFB1-initiated animals fed control diet, whereas PFOS caused a minor increase in liver tumor incidence. E2 and PFOA also enhanced MNNG-initiated hepatocarcinogenesis. Pearson correlation analyses, unsupervised hierarchical clustering and principal components analyses showed that the hepatic gene expression profiles for E2 and PFOA, PFNA, PFDA and PFOS were overall highly similar, though distinct patterns of gene expression were evident for each treatment, particularly for PFNA. Conclusions: Overall, these data suggest that multiple PFAAs can promote liver cancer and that the mechanism of promotion may be similar to that for E2.

overall_design: A total of 40 samples were analyzed using a a dye-swap, reference sample hybridization protocol.  Rainbow trout were exposed to the following experimental treatments via the diet for two weeks (number in parenthesis is assigned group #): (1) Control; (2) 5 mg/kg diet estradiol (E2); (3) 2000 mg/kg diet perfluorooctanoic acid (PFOA); (4) 2000 mg/kg diet perfluorononanoic acid (PFNA); (5) 2000 mg/kg diet perfluorodecanoic acid (PFDA); (6) 200 mg/kg diet perfluorooctane sulfonate; (7) 2000 mg/kg 8:2 fluorotelomer alcohol (FTOH); and (8) 2000 mg/kg diet clofibrate.  A total of 40 total hepatic mRNA samples were analyzed using a dye-swap, reference sample hybridization protocol.  A reference RNA pool was made by combining equal amounts of RNA from all control RNA samples, with one exception. A separate time-matched reference pool was utilized for group 6 samples (PFOS treatment).  Five hybridizations were performed for each treatment group in the following pattern: Replicate A Cy5/Reference Cy3; Replicate A Cy3/Reference Cy 5; Replicate B Cy5/Reference Cy3; Replicate B Cy3/Reference Cy5; Replicate C Cy5/Reference Cy3. Thus, the experiment consisted of three biological replicates, for two of which were replicated technically.

first: Gayle

last: Orner

first: Cari

last: Buchner

first: Jerry

last: Hendricks

first: Aaron

last: Duffy

first: David

last: Williams


title: Kinetic analysis of carolacton regulated genes

city: Braunschweig

first: Michael

last: Reck

address: Inhoffenstr. 7

department: Microbial Communication

country: Germany

institute: Helmholtz Centre for Infection Research

summary: Transcriptional profiling of carolacton treated S. mutans biofilm cells in comparison to untreated biofilms in a time series approach.

overall_design: Two condition times series experiment, carolacton treated vs. untreated for timepoints 20, 40, 60, 120 and 300 minutes post carolacton addition, 2 technical replicates of each sample (dye swap), conditions 20, 60, 300 Min in 3 biological replicates, condition 120 Min in 2 biological replicates, condition 40 min one biological sample

first: Jürgen

last: Tomasch

first: Irene

last: Wagner-Döbler


title: Lactobacillus plantarum IMDO 130201, a wheat sourdough isolate, adapts to growth in wheat sourdough simulation medium at different pH values through differential gene expression

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Sourdough is a very competitive and challenging environment for microorganisms. Usually, a stable microbiota composed of lactic acid bacteria (LAB) and yeasts comes to dominate this ecosystem. Although rich in carbohydrates, thus providing an ideal environment to grow, the low pH presents a particular challenge. The nature of the adaptation to this low pH was investigated for Lactobacillus plantarum IMDO 130201, an isolate from a laboratory wheat sourdough fermentation. Batch fermentations were carried out in wheat sourdough simulation medium, and total RNA was isolated from mid-exponential growth phase cultures, followed by differential gene expression analysis using a LAB functional gene microarray. At low pH values, an increased expression of genes involved in peptide and amino acid metabolism was observed as well as of genes involved in plantaricin production and lipoteichoic acid synthesis. The results highlight cellular mechanisms that allow L. plantarum to function at a low environmental pH.

platform_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

overall_design: The labeled aRNA samples were hybridized using a loop design, i.e. two consecutive samples (e.g., pH 3.5 and pH 4.0, pH 4.0 and pH 4.5, etc.) were hybridized on the same microarray slide, each labeled with another fluorescent dye (Cy3 or Cy5), and the loop was closed by hybridizing sample pH 5.5 together with sample pH 3.5.

first: Gino

last: Vrancken

first: Luc

last: De Vuyst

first: Tom

last: Rimaux

first: Joke

last: Allemeersch

first: Paul

last: Van Hummelen

first: Stefan

last: Weckx


title: affy_cinetique_lyon_rose: Flower/Petal initiation and development in roses

status: Public on Sep 01 2011

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary:
affy_cinetique_lyon_rose. The objective is to identify genes involved in petal development and senescence. R. chinensis cv Old Blush (OB) was used for the following reasons: it is a diploid Chinese rose that participated in the generation of modern roses (recurrent flowering, scent, etc.). The objective here is to identify genes whose expression is associated with different flower development stages, from floral meristem to senescing flower. These genes are putative candidates involved in floral initiation, development and senescence. All samples were collected at the same time early in the afternoon. Meristems and early flower development stages were dissected under a microscope. Total RNA was extracted from harvested tissues using the Plant RNA kit (Macherey Nagel), and then used to hybridize Rosa-Affymetrix microarrays.

Keywords: time course

overall_design:
12 arrays - rose
6 developmental stages, 2 replicates each.

first: Sandrine

last: Balzergue

first: Mohammed-

last: Bendahmane

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Anti-inﬂammatory eﬀects of tetradecylthioacetic acid (TTA)  in macrophage-like cells from Atlantic salmon (Salmo salar  L.)

city: aas

first: Fabian

last: Grammes

address: Arboretvn. 2

department: CIGENE

country: Norway

institute: Norwegian University of Life Sciences

summary:
Background: Commercial Atlantic salmon is fed diets with high fat levels to promote fast and cost-eﬀective growth. To avoid negative impact of obesity, food additives that stimulate fat metabolism and immune function are of high
interest. TTA, tetradecylthioacetic acid, is a synthetic fatty acid that stimulates mitochondrial β -oxidation most likely by activation of peroxysome proliferator-activated receptors (PPARs). PPARs are important transcription factors regulating multiple functions including fat metabolism and immune responses. Atlantic salmon experiments have shown that TTA supplemented diets signiﬁcantly reduce mortality during natural outbreaks of viral diseases, suggesting a modulatory role of the immune system.

Results: To gain new insights into TTA eﬀects on the Atlantic salmon immune system, a factorial, high-throughput microarray experiment was conducted using a 44K oligo nucleotide salmon microarray SIQ2.0 and the Atlantic salmon macrophage-like cell line ASK. The experiment was used to determine the transcriptional eﬀects of TTA, the eﬀects of TTA in poly(I:C) elicited cells and the eﬀects of pretreating the cells with TTA. The expression patterns revealed that a large proportion of genes regulated by TTA were related to lipid metabolism and increased mitochondrial β -oxidation. In addition we found that for a subset of genes TTA antagonized the transcriptional eﬀects of poly(I:C). This, together with the results from qRT-PCR showing an increased transcription of anti-inﬂammatory IL10 by TTA, indicates anti-inﬂammatory eﬀects.

Conclusions: We demonstrate that TTA has signiﬁcant eﬀects on macrophage-like salmon cells that are challenged by the artiﬁcial dsRNA poly(I:C). The immune stimulatory eﬀect of TTA in macrophages involves increased lipid metabolism and suppressed inﬂammatory status. Thus, suggesting that TTA directs the macrophage-like cells towards alternative, anti-inﬂammatory, activation. This has positive implications for TTA as a feed additive.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Factorial designed experiment: factor pretreatment = 2 levels (Control, TTA); factor treatment = 4 levels (Control, TTA, polyIC, TTA+polyIC). Experiment was performed with 2 biological replicates (different passages). 1 array hybridization failed and was excluded from the dataset. Therefore total number of arrays =15

first: Harald

last: Takle


title: Acute ITP vs. Chronic ITP (Children)

city: Palo Alto

first: Bing

last: Zhang

state: CA

address: 3373 Hillview Ave

institute: Stanford University

summary: Whole blood transcriptional profiling of pediatric idiopathic thrombocytopenic purpura (ITP) patients comparing self-limited acute ITP patients with chronic ITP patients or progression-to-chronic ITP patients.

overall_design: Patient samples were collected during 3 different disease states: 8 samples from acute ITP pts (within 6 months of dx, during active disease), 4 samples from progression-to-chronic ITP pts (within 6 months of dx), and 14 samples from chronic ITP (after 6 months of dx).

first: Ruchira

last: Sood


title: Transition from succinate to methanol growth in Methylobacterium Extorquens AM1

city: Seattle

first: Elizabeth

last: Skovran

state: WA

address: 616 NE Northlake Place, Benjamin Hall Rm 440

department: Chemical Engineering

institute: University of Washington

summary:
In order to provide information about the gene expression response that occurs when cells experience a change in carbon source, succinate limited chemostat cultures of Methylobacterium extorquens AM1 were grown to and maintained at an OD of ~0.63, transferred to flasks and methanol was added.  Cells were harvested for RNA extraction at time: 0 min, 10 min, 30 min, 1 hr, 2 hr, 4 hr and 6 hr post transition.  At 30 min, a no methanol addition sample was extracted as a carbon starvation control.  These data were used in conjunction with flux, enzymatic and metabolite measurements to assess the changes in central metabolism during this transition.
Abstract from manuscript: When organisms experience environmental change, how does their metabolic network reset and adapt to the new condition? This study focused on the mechanisms of metabolic adaptation occurring during the transition from succinate to methanol growth by the methylotrophic bacterium Methylobacterium extorquens, analyzing changes in carbon flux, gene expression, metabolites and enzymatic activities over time. Initially, cells experienced metabolic imbalance with excretion of metabolites, changes in nucleotide levels and cessation of cell growth. Though assimilatory pathways were induced rapidly, a transient block in carbon flow to biomass synthesis occurred, and enzymatic assays suggested methylenetetrahydrofolate dehydrogenase as one control point. This “downstream priming” mechanism ensures that significant carbon flux through these pathways does not occur until they are fully induced, precluding the buildup of toxic intermediates. Most metabolites that are required for growth on both carbon sources did not change significantly, even though transcripts and enzymatic activities required for their production changed radically, underscoring the concept of metabolic setpoints.

overall_design: Gene expression in succinate limited chemostat cultures was compared to gene expression in cells transferred to flasks before and after methanol addition. As a control, a time = 0 sample (RNA prepared from cells harvested directly from the chemostat) was compared to a time = 0 sample immediately obtained after the cells were transferred to flasks, before methanol was added in order to identify changes due to flask transfer.  A carbon starvation control was also done comparing expression from time = 0 (chemostat cells) to cells transferred to flasks for 30 min with no carbon source added.  Two biological replicates each with two techinal replicates (dye swap) were analyzed for time = 0 (chemostat) vs 10 min, 30 min, 1 hr and 2 hr after methanol addition.  One biological replicate with two technical replicates (dye swap) were analyzed for  time = 0 (chemostat) vs time = 0 (flask transfer), and time = 0 (chemostat) vs time = 4 hr, 6 hr and 30 min no methanol addition.


title: SG200 vs. SG200 delta-tup1

city: Sevilla

first: Jose

last: Ibeas

address: Carretera de Utrera Km 1

department: Biolgía Molecular e Ingeniería Bioquímica

institute: Universidad Pablo de Olavide

summary: We use this array to determine genes under the control of the transcriptional regulator Tup1

overall_design: We have compare the overal gene expression in wild type strain in compare to a mutant harbouring Tup1 deletion. Cells were grown on charcoal containing minimal media for 48h before total RNA extraction.

first: A

last: Elías-Villalobos

last: Fernández-Alvárez

first: J


title: BAC-microarrays aCGH data from 67 Ewing's Sarcoma tumor samples and 16 Ewing's Sarcoma cell lines

city: Salamanca

first: Carlos

last: Mackintosh

address: Campus Miguel de Unamuno S/N

institute: Centro de Investigación del Cáncer

summary: 67 tumor samples were aCGH profiled in order to obtain frequencies of recurrent copy number alterations intended to posterior correlations with clinical data. 16 cell lines were characterized as well.

overall_design: Whole genomic DNA from all samples was Cy5 labeled and co-hybridized onto BAC-microarrays along with a Cy3-labeled pool of 100 healthy donors' DNA


title: Comparative genomic hybridization study of Neisseria meningitidis

status: Public on Jul 31 2011

first: John

last: Braisted

summary:
PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships.

The Neissiria are among most deadly pathogens world-wide. The infections and outbreaks caused by this pathogens is quite frequent despite existing diagnostic network and therapeutic means. Therefore, developing reliable diagnostic tools and efficient (broad-spectrum) therapeutics for  Neisseria meningitidis  remain a public health priority for every country in world today.

The comparative genomics study will provide the largest hitherto genomic data sets regarding this pathogen.These large data sets will enable us as well as other members of scientific community to conduct comprehensive data mining in the form of gene association studies with statistical power and significance.

overall_design: Two hundread fifty query strains were investigated in this study, with each query strain hybridized against the reference strain, MC58.  Each strain has a single dye experiment.  Each oligo is spotted on the N. meningitidis species microarray once.  Positive controls on the array consist of oligos designed from the sequenced reference genome of N. meningitidis and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.

first: Leka

last: Papazisi

first: Erik

last: Snesrud

first: Pratap

last: Venepally

first: Sarah

last: Akkoush

first: Adrian

last: Pineda

first: Eric

last: Wester

first: M

last: Kim

first: Lakshmi

last: Viswanathan

first: Dana

last: Busam

first: Jia

last: Liu

first: Alex

last: Saeed

first: Malene

last: Bek-Thompsen

first: Bernard

last: Beal

first: Mogens

last: Kilian

first: Tatiana

last: Dracheva

first: Robert

last: Fleischmann

first: Scott

last: Peterson


title: Microarray evidence for off target effects and the optimisation of targeted RNAi mediated gene silencing in the cattle tick Rhipicephalus (Boophilus) microplus

city: Brisbane

first: Ala

last: Lew-Tabor

state: Queensland

address: 306 Carmody Rd, St Lucia

department: Queensland Alliance for Agriculture and Food Innovation

country: Australia

institute: The University of Queensland

summary: The NimbleGen cattle tick custom microarray based on the BmiGI.V2 database of R. microplus ESTs was used to screen the resulting mRNA harvested from ticks treated with the tick Ubiquitin-63E 600bp dsRNA in comparison to controls. A total of 144 ESTs including TC6372 (Ubiquitin-63E) were down-regulated with 136 ESTs up-regulated following treatment.  The results obtained substantiated the knockdown phenotype with ESTs identified as associated with ubiquitin proteolysis as well as oogenesis, embryogenesis, fatty acid synthesis and stress responses. A stringent bioinformatics analysis was undertaken to predict off target effects (OTE) resulting from the in silico dicing of the 600bp Ubiquitin-63E dsRNA which identified 10 down (including TC6372) and 13 up-regulated ESTs within the list of differentially expressed probes on the microarrays. Subsequent knockdown experiments utilising 196bp and 109bp dsRNAs, and a cocktail of short hairpin RNAs targeting Ubiquitin-63E demonstrated similar phenotypes for the dsRNAs but nil effect following shRNA treatment. Quantitative real time PCR analysis confirmed TC6372 and predicted off target differential expression.  Our study demonstrates the effectiveness and specificity for utilising ~100bp dsRNA products for targeted tick gene knockdown with nil identified off targets.

overall_design: The microarray was conducted by NimbleGen Systems Inc following the method reported by Saldivar [Saldivar L et al., Insect Mol Biol 2008, 17(6):597-606]. Briefly, Custom high-density single channel oligonucleotide arrays were constructed by NimbleGen Systems Inc. using 13 601 of the 13 643 members of BmiGI Version 2 with 14 perfect match 50-mer probes per BmiGI target. No mismatched probes were included on the arrays, although probes with randomly generated sequences were included. These random sequence probes were designed to match the melting temperature (Tm) of the other probes on the array and to reflect the distribution of non-specific signal intensities for binding events to probes with approximately the same composition as the perfect match probes but with random sequences. The associated GEO dataset can be found online at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6373. Each microarray chip includes two in-slide replicates (spot replicates). In this experiment two biological replicates for each sample were hybridized to assess variability between individual samples. Each pooled sample consisted of 30 female adult ticks (N strain) as the source of RNA. Four technical replicates were processed, i.e. repeated measurements of the same pooled R. microplus mRNA, consisting of two chip replicates with two spot replicates. The chip replicates were hybridized on different dates to different chips, while spot replicates indicate the same probe was spotted on different locations on the chip. Four R. microplus samples were hybridized to separate microarrays at NimbleGen Systems Inc. (Madison, WI, USA). Data Processing: Statistical analysis  Following array hybridization the raw intensity values were background corrected using convolution and normalized using quantile normalization to adjust for technical sources of variation. Final log2 expression intensities were generated using the Robust Multichip Average (RMA) algorithm [Irizarry et al.,Biostatistics 2003, 4:249-264]; [Groeneveld E, et al.,Proceedings 6th World Cong Genet Appl Livest Prod,: 1998; Armidale, NSW, Australia;  455-458] implemented in R. Differential expression was tested on the RMA normalized intensities using a mixed model of the form yijkr=μ+BSrk+Gi+GTij+Eijkr where yijkr are the log2 RMA normalized signal intensities; i =gene, j=treatment, r=block, k=slide/array, the main fixed effect is BSrk (block by slide interaction), Gi is the main random effect of the gene; GTij is the random interaction term of the gene by treatment; E is just the error term; and normal assumptions for the random effects – iid are assumed. The model was fitted using VCE4.0 [Groeneveld E, et al., 1998]. Differentially expressed (DE) probes were considered as those which were three or more standard deviations away from the mean (p-value <0.001).  The contrast of interest was the 600pb dsRNA microinjected ticks (R. microplus Ubiquitin-63E homologue as per Kurscheid et al 2009, BMC Molecular Biology 10:26) compared to normal untreated controls in order to examine the knockdown effect associated with phenotype. Kurscheid et al 2009 reported a strong knockdown phenotype following dsRNA knockdown and the subsequent differentially expressed ESTs were examined in this array experiment. The putative identities of the lists of up and down regulated tick sequences (DE probes) were then subsequently analysed using bioinformatic tools to predict function (described below). Bioinfomatics: Nimblegen tick microarray differentially expressed probes with fold changes >1.5 and p-value <0.001 were screened against the following databases on the CCG [Centre for Comparative Genomics: http://ccg.murdoch.edu.au], Grendel HPC system [Hunter A, et al.,Australasian Workshop on Grid Computing and e-Research 2005:2-3]; NCBI protein (nr and patent) [National Centre for Biotechnology Information: http://www.ncbi.nlm.nih.gov], String [Mering von C., et al.,Nucleic Acids Research 2006:00: D01-D05], COG [Tatusov R, et al., BMC Bioinformatics 2003, 4], tigr_bmigi.062608 [Wang et al.,BMC Genomics 8:368], NCBI Conserved Domain database [Goonesekere N, et al., Proteins 2008, 71(2):910-919], and KEGG (Kanehisa & Goto 2000 Nucleic Acids Res. 28, 27-30; Kanehisa et al 2006 Nucleic Acids Research 34, D354-D357; Kanehisa et al 2010 Nucleic Acids Research 38, D355-D360).  Further analysis of differentially expressed transcripts identified in the microarray experiments was undertaken using the BLAST program suite (Altschul et al., 1997) for similarity searches in the UniProt database (TheUniProtConsortium, 2010 Nucleic Acids Res 38, D142-D148.) and in the protein sequence database of Ixodes scapularis tick (available from http://www.vectorbase.org/Ixodes_scapularis/Info/Index; last accessed 2010-11-21). The results of the blastx searches against the I. scapularis protein sequences where used to map the R. microplus ESTs to unique identifiers in the DAVID Bioinformatics Resource and perform a subsequent functional annotation to Gene Ontology terms in the categories “Biological Process (BP)”, “Cellular Component (CC)”, and “Molecular Functions (MF)” (Dennis et al 2003 Genome Biology 4: P3; Huang et al 2009 Nature Protoc. 4: 44-57.).

first: Cedric

last: Gondro

first: Sebastian

last: Kurscheid


title: Examine gene expression in maize pulvini in gravitropsim

city: Glen Osmond

first: Qisen

last: Zhang

state: South Australia

address: Waite Campus

department: School of Agriculture, Food and Wine

institute: University Of Adelaide

summary: A gradient cell elongation with maximum in the lower  side of pulvini and minimum in the upper side of pulvini pushes a maize stem upwards from a horizontal to a vertical position during gravitropsim. A differentiated gene expression between lower and upper pulvini was examined at 1 h, 6 and 24 h.

overall_design: Gene expression levels were compared in control (not bending), lower and upper (bending) pulvini. The samples were harvested at 1 h, 6 h and 24 h gravitropsim and total RNA were extracted using for microarray experiment.

first: Geoffrey

last: Fincher

first: Kanwarpal

middle: S

last: Dhugga

first: Antoni

last: Rafalski

last: Tingey

first: Kevin

middle: R

last: Hayes

first: Mary

last: Beatty


title: Murine Kidney cells: Control versus Ischemia reperfusion injury

city: Boston

first: John

last: Iacomini

address: 800 Washington st

institute: Tufts University/ Medical Center

summary: miRNA profiling of kidney tissue from C57BL/6 mice that received a 30 minute ischemic injury compared with control kidney tissue from mice that received sham operation only.

overall_design: Two condition experiment -  sham and ishemic injury (IRI).  Eight time points were measured using pooled samples from three mice.

first: Stefan

last: Tullius


title: Bovine in-vitro blastocysts vs granulosa cells

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary: Transcriptional profiling of bovine in-vitro produced blastocysts at day 7 and granulosa cells collected at day 8 to 11 post-eostrus of lactating cows.

overall_design: Two-condition experiment, in-vitro Blastocyst vs. Granulosa cells. Biological replicates: 3 . One replicate per array. Dye swap experiment, two-colors.

first: Claude

last: Robert

first: Julie

last: Nieminen

first: Isabelle

last: Dufort

first: Jason

last: Grant

first: Gael

last: Cagnone

first: Dany

last: Plourde

first: Anne-Laure

last: Nivet

first: Eric

last: Fournier

last: Paquet

first: Michal

last: Blazejczyk

first: Philippe

last: Rigault

first: Nicolas

last: Juge

first: Marc-Andre


title: miRNA expression data from human high and low risk prostate carcinoma

city: Wuerzburg

first: Burkhard

middle: Gerhard

last: Kneitz

address: Oberdürrbacher Str. 6

department: Klinik und Poliklinik für Urologie und Kinderurologie

institute: University of Wuerzburg

summary:
miRNA expression of 6 high risk and 8 low risk prostate carcinoma were compared to the expression of 6 benign prostatic hyperplasia.

Keywords: expression profile

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We used microarrays to detail the global programme of miRNA expression underlying tumorigenesis and tumor progression and identified dysregulated genes during this process

first: Martin

last: Spahn

first: Susanne

first: Nico

last: Stenger

first: Claus-Jürgen

last: Scholz

first: Philipp

last: Ströbel

first: Hubertus

last: Riedmiller


title: Analysis of carolacton regulated genes

first: Michael

last: Reck

summary: Transcriptional profiling of carolacton treated S. mutans biofilm cells in comparison to untreated biofilms after 8h of growth.

overall_design: Two condition experiment, carolacton treated vs. untreated, biological replicates: 4, 2 technical replicates of each sample (Dye Swap)

first: Jürgen

last: Tomasch

first: Irene

last: Wagner-Döbler


title: Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features.

status: Public on Jul 28 2011

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

institute: CRCM

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In metazoans, thousands of DNA replication origins (Oris) are activated to replicate DNA at each cell cycle. Although their timing of activation is better understood, their genomic organization and their genetic nature remain elusive. Here, we identified Oris by nascent strand (NS) purification and characterized their common features by performing a genome-wide analysis in both Drosophila and mouse cell lines. We show that in both species most CpG islands (CGI) contain Oris, although methylation is nearly absent in Drosophila, suggesting that this epigenetic mark is not crucial for defining the initiation event. Moreover, nascent strands at the borders of CGIs show a striking bimodal distribution, suggestive of a dual initiation event. We also found that Oris contain a unique nucleotide skew around NS peaks, characterized by G/T and C/A over-representation at 5’ and 3’ of the Ori sites, respectively. GC-rich elements are detected, which are good predictors of Oris, in both mouse and Drosophila, suggesting that common sequence features are part of metazoan Oris. In the heterochromatic chromosome 4 of Drosophila, Oris are strongly correlated with HP1 binding sites. At the chromosome level, we show that Oris are organized in Ori-rich and -poor regions that co-localize with early and late replicating domains, respectively. Finally, the genome-wide analysis was coupled with a DNA combing analysis of the in-vivo spacing of replication origins. The results suggest that Oris are in large excess, and organized in groups of site-specific but flexible origins that define replicons, where a single origin is used in each group. This organization provides both site specificity and Ori firing flexibility in each replicon, allowing possible adaptation of DNA replication to environmental cues and cell fates.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design:
Cells:
MEFs were derived from 13.5-day mouse embryos and used at passage 4 or 5. P19 cells and ES cell line CGR8 are pluripotent embryonic mouse cells. Kc cells are were embryonic Drosophila cells. Two biological independent samples for Drosophila, four independent samples for P19 cells, three independent samples from ES and three for MEF cells were used.For control drosophila Kc G2/M arrested cells, cells were synchronized in prometaphase by incubation with 4 mM thymidine overnight, release in fresh medium for 4 hours and incubation with nocodazole overnight.
Nascent Strand preparation:
Dividing cells (2.5-5 ×108) were lysed in DNAzol (Invitrogen) and digested with 200 μg/ml proteinase K. DNA was precipitated with ethanol and resuspended in 2 ml TEN20. Denatured genomic DNA was loaded onto a 30 ml neutral 5 to 30% sucrose gradient prepared in TEN300. Fractions corresponding to 0.5-2.5 kb were pooled and phosphorylated with T4 polynucleotide kinase (PNK) and digested with lambda exonuclease. NS were subjected to one or two further cycles of T4 PNK phosphorylation and lambda exonuclease digestion. Finally, NS were purified using the CyScribe GFX Purification Kit and amplified using the WGAII kit (Sigma). Hybridization, washing and scanning of microarrays were done by Nimblegen Service Laboratory.
Microarray Design:
Drosophila melanogaster samples were hybridized using 2.1M Nimblegen microarrays (Design ID 6262). These tiling arrays contain in total 2,164,511 oligonucleotide probes representing the non-repetitive regions of the Drosophila melanogaster genome (chromosome 2L, 2R, 3L, 3R, 4 and X; Flybase release 4.3).
All the processed data (GSM720962, GSM721024) were generated using the BDGP/Flybase release 4 of the Drosophila melanogaster genome assembly (UCSC dm2, April 2004).
Mouse samples were hybridized using the Nimblegen 389K tiling arrays (Design ID 4095) which cover 60.4 Mb of non-repetitive DNA sequences in chromosome 11 (56.6-117 Mb). All the processed data (GSM718701, GSM718735, GSM718744) were generated using the UCSC mm8 (NCBI Build 36, February 2006) of the Mus musculus genome assembly.
Data normalization processed data compilation:
Experimental (Cy5) and control (Cy3) signal intensities quantified and provided by Nimblegen were converted into log2 ratios (log2 (Cy5/Cy3)). The Lowess normalization method was applied to eliminate intensity-dependent variations in dye bias (Yang et al. 2002). A sliding median window with a length of 5 oligonucleotide probes was used to smooth the signal. Mode (m) and s (median absolute deviation) of normalized log2 ratios were computed. Assuming that the normal distribution (specified by m and s) covered the entire background noise (non-significant signals), for each probe, one p-value was computed by applying the false discovery rate (FDR) correction (Benjamin and Hochberg 1995). To create processed data, normalized log2 ratios of replicate samples were combined by averaging the values at the corresponding genomic positions and the corrected p-values were combined using a Chi-Square distribution (Fisher 1932).

last: Coulombe

first: Alice

last: Vigneron

first: Aurore

last: Puy

first: Sabine

last: Laurent-Chabalier

first: Marcel

last: Méchali


title: Cdc14 as transcription regulator of RNA pol-II

status: Public on Jul 29 2011

city: London

first: Adam

last: Giess

address: Hammersmith Hospital, Du Cane Road

institute: MRC Clinical Sciences Centre

type: Expression profiling by genome tiling array

summary: In yeast, the phosphatase Cdc14 is required for mitotic exit and for segregation of repetitive regions. Cdc14 is also a subunit of the silencing complex RENT, but no roles in transcription repression have been described. Here we report that Cdc14 promotes silencing at the integenic spacer sequences (IGS) of ribosomal genes during interphase and at Y' repeats in sub-telomeric regions during mitosis, through its ability to dephosphotylate the CDT domain of the RNA polymerase II.

overall_design: CDC14 and CDC15 strains were grown at 25°C and 37°C. Comparisons were made between each strain at different temperatures, and between strains at the same temperature.

first: Luis

last: Aragón

first: Andrés

last: Clemente-Blanco


title: FREP3 is a determinant of resistance to schistosome infection in snails

status: Public on Jul 30 2011

city: Albuquerque

first: Michelle

middle: A.

last: Forys

state: NM

address: MSC03 2020, 1 University of New Mexico

department: Biology

institute: University of New Mexico

summary: Transcriptional profile of snails exposed to irradiated E. paraensei miricidia and four days later challenged with S. mansoni miricidia.  Compared to snails exposed to only irradiated E. paraensei miricidia.

overall_design: Each replicate is comprised of 1 individual snail from the specified treatment group.  Six replicates of each treatment were analyzed on the Snail oligo array.

first: Patrick

last: Hanington


title: Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analysis

city: Urbana

first: Yujie

last: Men

address: 205 N Mathews Ave

institute: University of Illinois at Urbana-Champaign

summary: The syntrophic growth of strain 195 with Desulfovibrio vulgaris Hildenborough (DVH) and/or Methanobacterium congolense (MC) enhanced TCE dechlorination process by faster dechlorination rate and more robust growth.  Transcriptomes of strain 195 grown in isolation, co- and tri-cultures were obtained by microarray experiments to find out the differential expressed genes corresponding to the syntrophic growth.  Thus we can better understand the role of DVH and MC within this syntrophy.

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: [Transcriptomic analysis]: Cells of pure strain 195 culture, co-culture and tri-culture were collected at the early exponential phase during TCE dechlorination process for RNA extraction, cDNA synthesis, fragmentation, labelling, and hybridization on microarray.  We sought to obtain differential transcription of 195 genes in pure, co- and tri- cultures, in order to understand the role of DVH and MC in the syntrophy of strain 195.

first: Helene

last: Feil

first: Nathan

last: VerBerkmoes

first: David

last: Johnson

middle: K

last: Lee

first: Kimberlee

last: West

first: Stephen

middle: H

last: Zinder

first: Gary

last: Andersen

first: Lisa

last: Alvarez-Cohen


title: The role of Stk in Streptococcus pyogenes

city: Atlanta

first: Julia

last: Bugrysheva

state: GA

address: 1510 Clifton Rd Rm 3076

department: Department of Microbiology

institute: Emory Univeristy

summary: Transcriptional profile of Streptococcus pyogenes stk mutant strain JRS2516 vs its wild type parent strain MGAS2221

overall_design: The RNA prepared from triplicate cultures for the wild type and the stk mutant strains was each labeled with Cy3 and hybridized to duplicate arrays. Reference RNA consisted of pooled RNA for the wild type and stk mutant, labeled with Cy5.


title: Lipopolysaccharide (LPS) response in macrophages from MD-2-deficient mice

city: Malmö

first: Harry

last: Björkbacka

address: CRC 91:12, UMAS entrance 72

department: Dept. of Clinical Sciences, Malmö

country: Sweden

institute: Lund University

summary: Lipid A (a hexaacylated 1,4  bis-phosphate) is a potent immune stimulant for TLR4/MD-2. Upon lipid A ligation, the TLR4/MD-2 complex dimerizes and initiates signal transduction. Historically, studies also suggested the existence of TLR4/MD-2-independent LPS signaling. Here we define the role of TLR4 and MD-2 in LPS signaling by using genome wide expression profiling in TLR4- and MD-2-deficient macrophages after stimulations with peptidoglycan-free LPS and synthetic E.coli lipid A. Of the 1,396 genes found significantly induced or repressed by any one of the treatments in the wildtype macrophages, none was present in the TLR4- or MD-2-deficient macrophages, confirming that the TLR4/MD-2 complex is the only receptor for endotoxin, and are both absolutely required for responses to LPS. Using a molecular genetics approach, we investigated the mechanism of TLR4/MD-2 activation by combining the known crystal structure of TLR4/MD-2 with computer modeling. We used lipid IVa, a defined lipid A mimetic to model the activation of mouse TLR4/MD2. The two phosphates on lipid A were predicted to interact extensively with the two positively charged patches mouse TLR4 according to our dimeric murine TLR4/MD-2/lipid IVa model. These two patches are composed of K263, R337, and K360 (Positive Patch 1), and K367 and R434 (Positive Patch 2). When either Positive Patch was abolished by mutagenesis into Ala, the responses to LPS and lipid A were almost abrogated. Thus, ionic interactions between the two phosphates on lipid A and the two positively charged patches on murine TLR4 appear to be essential for LPS receptor activation.

overall_design: The gene expression profile of macrophages from C57BL/6 and MD-2-deficient mice following either 10 ng LPS /mL, 100 ng lipid A/mL or 10 nM Pam2 stimulation for 2 hours were compared to PBS-stimulated control cells . In vitro differentiated macrophages from two individual WT and MD-2-deficient mice were cultured and stimulated with agonists separately, comparing the gene expression to PBS-stimulated control cells from the same mouse. Comparisons of PBS-stimulated WT cells to PBS-stimulated MD-2-deficient cells were performed to directly compare basal gene expression in the two genotypes.

first: Jianmin

last: Meng

first: Mei

last: Gong

last: Bjorkbacka

first: Douglas

middle: T

last: Golenbock


title: Expression data from Aspergillus oryzae grown under hypoxic condition.

city: Tsukuba

first: Yasunobu

last: Terabayashi

institute: Tsukuba University

summary: Hypoxia imposes stress on filamentous fungi that require oxygen to proliferate. Global transcription analysis of Aspergillus oryzae grown under hypoxic conditions found that the expression of about 50% of 4,244 affected genes was either induced or repressed more than 2-fold. A comparison of these genes with the hypoxically-regulated genes of A. nidulans (Masuo et al., Mol. Gen. Genet. 2010, 284:415-424) based on their predicted amino acid sequences classified them as bi-directional best hit (BBH), one-way best hit (extra homolog: EH) and no-hit (non-syntenic genes: NSG) genes. Clustering analysis of the BBH genes indicated that A. oryzae and A. nidulans down-regulated global translation and transcription under hypoxic conditions, respectively. Under hypoxic conditions, both fungi up-regulated genes for alcohol fermentation and the γ-aminobutyrate shunt of the tricarboxylate cycle, whereas A. oryzae up-regulated the glyoxylate pathway, indicating that both fungi eliminate NADH accumulation under hypoxic conditions. The A. oryzae NS genes included specific genes for secondary and nitric oxide metabolism under hypoxic conditions. This comparative transcriptomic analysis discovered common and strain-specific responses to hypoxia in hypoxic Aspergillus species.

overall_design: We transferred A. oryzae cells from normoxic to hypoxic conditions for 6 h, and then back to normoxic conditions to examine the effect of hypoxia on gene expression. Total RNA was prepared for DNA microarray analysis from the cells after 1, 3, and 6 h of exposure to hypoxia, followed by 1, 3, and 6 h of reoxygenation.

first: Tatsuya

last: Kitazume

first: Shunsuke

last: Masuo

last: Fujii

first: Naoki

last: Takaya


title: Variability of gene expression profiles in human blood and lymphoblastoid cell lines

status: Public on Jul 26 2011

city: Oxford

first: Josine

last: Min

address: Roosevelt Drive

institute: The Wellcome Trust Centre for Human Genetics

summary: Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However, cell and RNA isolation procedures and the variety of cell types that make up whole blood can affect gene expression measurements. We therefore systematically investigated global gene expression profiles in peripheral blood from six individuals collected during two visits by comparing five of the following cell and RNA isolation methods: whole blood (PAXgene), peripheral blood mononuclear cells (PBMCs), lymphoblastoid cell lines (LCLs), CD19 and CD20 specific B-cell subsets. Gene expression measurements were clearly discriminated by isolation method although the reproducibility was high for all methods (range ρ = 0.90-1.00). The PAXgene samples showed a decrease in the number of expressed genes (P<1*10-16) with higher variability (P<1*10-16) compared to the other methods. Differentially expressed probes between PAXgene and PBMCs were correlated with the number of monocytes, lymphocytes, neutrophils or erythrocytes. The correlations (ρ =0.83; ρ =0.79) between the expression levels of detected probes were much lower compared to the two B-cell isolation methods (ρ =0.98). Gene ontology analysis of detected genes showed that genes involved in inflammatory responses are enriched in B-cells CD19 and CD20 whereas genes involved in alcohol metabolic process and the cell cycle were enriched in LCLs. Gene expression profiles in blood-based samples are strongly dependent on the predominant constituent cell type(s) and RNA isolation method. It is crucial to understand the differences and variability of gene expression measurements between cell and RNA isolation procedures, and their relevance to disease processes before application in large clinical studies.

overall_design: In the present study, we investigated variability and consistency in gene expression profiles between five of the most common post venipuncture methods of cell and RNA isolation: whole blood (PAXgene (PAX)), PBMCs, Epstein-Barr virus (EBV)  transformed LCLs, CD19-specific B-cells subsets (B-cell CD19), CD20-specific B-cells subsets (B-cell CD20). Using samples from six individuals collected during two visits, we evaluated the differences and concordances of global gene expression profiles, the biological and technical variability seen in these approaches, cell-type specific gene expression signatures and their relevance to large-scale biobanking initiatives.

first: Amy

last: Barrett

first: Tim

last: Watts

first: Fredrik

last: Pettersson

first: Helen

middle: E

last: Lockstone

first: Cecilia

middle: M

last: Lindgren

first: Jennifer

last: Taylor

first: Maxine

last: Allen

first: Krina

last: Zondervan

first: Mark

last: McCarthy


title: Comparison of transcriptome of in vitro and in vivo-produced bovine fetuses; specifically in liver and placental tissues.

city: New York

first: Le

last: Jiang

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

summary: During the past several decades, in vitro fertilization (IVF) has been increasingly used both in animal production and human infertility treatment. Animals derived from in vitro manipulation are occasionally associated with abnormal offspring syndrome (AOS) and other developmental abnormalities. By studying gene expression of in vitro-produced (IVP) embryos/animals, we gain an indicator of how well this procedure mimics the in vivo environment. Most previous studies of this nature have focused on only a few genes at a time or have been limited to studying the pre-implantation stage; thus, a global view of how gene transcription may be influenced by in vitro procedures during fetal development has yet to be ascertained. To this end, we collected liver and placental tissue samples from in vitro-produced and in vivo control bovine fetuses at day 90 and 180 of gestation. We used a bovine 13K oligonucleotide microarray to investigate the transcriptional profiles in both tissues and compared them with those of their age-matched in vivo counterparts. Surprisingly, in both liver and placental tissues, the transcriptional profiles between IVP and control fetuses, at either 90 or 180 days of gestation, were indistinguishable. A total of 879 genes were found to be significantly regulated during liver development from 90 to 180 days of gestation, but there were no gene expression changes in the placental tissue during this developmental period. Quantitative real time RT-PCR on 11 selected genes confirmed these results. Our results have certain implications for IVF technologies, both in agriculture and in human medicine.

overall_design: A total of 18 samples for each tissue type (liver & placenta) was analyzed (8 biological replicates for in vivo-produced fetuses and 10 biological replicates for in vitro ones). Two technical replicates were done for each sample.

first: Jiang

last: Le

first: Tian

last: X. Cindy


title: Monocyte gene expression patterns distinguish subjects with and without atherosclerosis.

city: Seattle

first: David

last: Pritchard

address: 815 Mercer Street Rm.  418

department: Pathology

institute: University of Washington

summary: We used microarrays to profile monocytes to identify gene expression differences correlating with disease status in carotid artery atherosclerosis.  We identified 1302 genes differentially expressed between control and affected subjects after correcting for clinical covariates.  Differential expression was likely caused by unidentified risk factors or systematic manifestations of atherosclerosis itself.

overall_design: Monocytes were extracted from subjects with and without carotid atherosclerosis.  Microarray hybridization was used to determine if expression patterns distinguish the subjects.

first: Steven

last: Schwartz


title: Transcriptomics evaluation of hexavalent chromium toxicity in human dermal fibroblasts

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

institute: National Institute for Occupational Safety and Health

summary: Significant occupational and environmental exposures to hexavalent chromium, a metal with broad toxicity potential in humans, have been reported. In order to understand the mechanisms of dermal toxicity induced by hexavalent chromium, global gene expression profiling of human dermal fibroblasts exposed to a toxic concentration of potassium dichromate was performed. Microarray analysis of the gene expression profile in the fibroblasts treated with potassium dichromate identified significant differential expression of approximately 1,200 transcripts compared with the control cells. Hierarchical cluster analysis of the gene expression profile demonstrated a clear separation of the treated cells from the control group of cells. Functional categorization of the differentially expressed genes identified the enrichment of genes involved in several cellular processes, including apoptosis and oxidative stress, in the fibroblasts exposed to hexavalent chromium. Induction of apoptosis and generation of hydroxyl radicals indicative of oxidative stress in the dermal fibroblasts in response to their exposure to hexavalent chromium were independently confirmed by TUNEL assay and electron spin resonance (ESR) analysis, respectively. The potassium dichromate-induced cytotoxicity, differential gene expression, apoptosis, and oxidative stress were significantly blocked by the addition of ferrous sulfate, an agent known for its ability to reduce hexavalent chromium to the insoluble and therefore impermeable trivalent form, to the cell culture medium. Taken together, our data provide insights into the potential mechanisms underlying the dermal toxicity of hexavalent chromium and suggest a definite role for apoptosis and oxidative stress in Cr(VI)-induced cytotoxicity in human dermal fibroblasts.

overall_design: 16 samples were analyzed in this experiment. Exponentially growing human dermal fibroblasts (3x105 cells) were cultured in T25 cell culture flasks. When the cells were approximately 70% confluent, hexavalent potassium dichromate (5µM) was added to the medium with or without 40µM ferrous sulfate. Following 16 hours of culturing at 37oC, total RNA was isolated for gene expression studies. Details of the samples are:     Control       4 Samples: Cr(0)-1, Cr(0)-2, Cr(0)-3, Cr(0)-4  Cr 5 µM     4 Samples: Cr(5)-5, Cr(5)-6, Cr(5)-7, Cr(5)-8  FeSO4 40 µM      4 Samples: Fe(40)-9, Fe(40)-10, Fe(40)-11, Fe(40)-12  Cr 5 µM + FeSO4 40 µM   4 Samples: Cr(5)+Fe(40)-13,Cr(5)+Fe(40)-14,                                                                      Cr(5)+Fe(40)-15, Cr(5)+Fe(40)-16

first: Christina

last: Umbright

first: Rebecca

last: Chapman

first: Stephen

last: Leonard

first: Shengqio

last: Li

first: Michael

last: Kashon

first: Pius

last: Joseph


title: Nitric oxide pathway specific gene alterations in inflammatory bowel disease

city: Stockholm

first: Linda

last: Gillberg

address: Gastro Research Lab M1:02

department: Medicine

institute: Karolinska Institutet

summary: Studying genes involved in the regulation of inflammation may help to clarify the pathogenesis of IBD. In search of the genes which products are known to be involved in NO signalling and altered in patients with IBD, our present aim was to determine the expression of such genes in CD and UC, respectively. To this end, microarray expression of genes known to be controlled by or which products are involved in NO signalling was studied in biopsies of colonic mucosa from patients and healthy controls.

overall_design: A cohort of inflamed colonic mucosa samples from 20 CD patients and 20 UC patients, as well as 6 control colonic mucosa samples, was used to acquire expression profiles. All of the inflamed samples were analysed individually, while the control samples were pooled and analysed in 4 replicates.

last: Varsanyi

first: Per

last: Hellström


title: Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors

status: Public on Jul 22 2011

city: Bethesda

first: Jennifer

last: Barb

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary: Topoisomerase I (Top1) relaxes both positive and negative supercoilings by producing transient Top1 cleavage complexes (Top1cc). Several studies have suggested the implication of Top1 in splicing. Here, we tested the implication of Top1cc in splicing at the global genome level in human carcinoma cells to determine whether Top1 inhibition selectively affects particular families of genes.

overall_design: We tested the impact of Top1 inhibition on splicing at the genome-wide level in human colon carcinoma HCT116 cells. The RNA of HCT116 cells treated with camptothecin (CPT) for various times was analyzed with ExonHit Human Splice Array.

first: Stéphanie

last: Solier

first: Barry

last: Zeeberg

first: Sudhir

last: Varma

first: Mike

last: Ryan

first: Kurt

last: Kohn

first: John

last: Weinstein

first: Peter

middle: J

last: Munson

first: Yves

last: Pommier


title: Distinct roles of ComK1 and ComK2 in gene regulation in Bacillus cereus (induced ComK1 or ComK2)

city: Jena

first: Akos

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

summary: Comparison of the Bacillus cereus with induced ComK1 (pATK31 in sample 1-3) or ComK2 (pATK32 in sample 4-6) proteins vs Bacillus cereus carrying empty plasmid (pLM5 in all samples)

overall_design: One condition design comparision of (IPTG induced overexpression construct vs IPTG induced empty plasmid) including a dye swap, 3 biological replicate

first: Aleksandra

last: Miroczuk

first: Oscar

last: Kuipers


title: Genomic Profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage (primary tumors and normal mammary glands)

status: Public on Jul 21 2011

first: Jeffrey

last: Green

address: Rm 4054, 37 Convent Drive

institute: NCI

summary: MicroRNAs (miRNAs) are small, non-coding, endogenous RNAs involved in many human diseases including breast cancer. miRNA expression profiling of human breast cancers has identified miRNAs related to the clinical diversity of the disease and potentially provides novel diagnostic and prognostic tools for breast cancer therapy. In order to further understand the roles of miRNAs in association with oncogenic drivers and in specifying sub-types of breast cancer, we performed miRNAexpression profiling on mammary tumors from eight well-characterized genetically -engineered Mouse (GEM) models of human breast cancer including MMTV–H-Ras, -Her2/neu, -c-Myc, -PymT, –Wnt1 and C3(1)/SV40 T/t-antigen transgenic mice, BRCA1fl/fl;p53+/-;MMTV-cre and the p53fl/fl ;MMTV-cre transplant model.

overall_design: miRNA expression data for 41 mouse primary mammary tumors and 5 mouse normal mammary glands

first: Min

last: Zhu

first: Ming

last: Yi

first: Chang

last: Kim

first: Chuxia

last: Deng

first: Yi

last: Li

first: Daniel

last: Medina

first: Robert

last: Stephen

first: Jeff


title: Distinct roles of ComK1 and ComK2 in gene regulation in Bacillus cereus (overexpressed ComK)

summary: Comparison of the Bacillus cereus with overexpressed Bacillus subtilis ComK (Bacillus cereus pNWcomKBsu)  vs Bacillus cereus carrying empty plasmid (Bacillus cereus pNW33N)


title: Circulating insulin-like growth factor (IGF)-1 Regulates Hippocampal IGF-1 Levels and Brain Gene Expression During Adolescence

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

summary: This study, using a growth hormone (GH)-deficient dwarf animal model and peripheral GH replacement, investigated the effects of circulating IGF-1 during adolescence on IGF-1 levels in the brain. Our results demonstrated that hippocampal IGF-1 protein concentrations during adolescence are highly regulated by circulating IGF-1, which were reduced by GH deficiency and restored by systematic GH replacement. In contrast, IGF-1 levels in the CSF were decreased by GH deficiency but not restored by GH replacement. Furthermore, analysis of gene expression using microarrays and RT-PCR indicated that circulating IGF-1 levels did not modify the transcription of IGF-1 or its receptor in the hippocampus but did regulate genes that are involved in microvascular structure and function, brain development, and synaptic plasticity, which potentially support brain structures involved in cognitive function during this important developmental period.

overall_design: GH-deficient dwarf (dw/dw) and heterozygous (HZ) rats were identified at postnatal day 33-34. Starting from d35, dw/dw rats received subcutaneous injection of either 300µg GH (dw/dw+GH) or saline (dw/dw+sal) for 7d or 30d. HZ animals received saline for the same periods as controls. Animals (n=4/group for each time point) were sacrificed, the hippocampi were dissected, and total RNA were isolated for subsequent transcriptomic profiling.

first: Han

last: Yan

first: Matthew

last: Mitschelen

last: Brucklacher

first: Georgina

middle: V

last: Bixler

first: Julie

middle: A

last: Farley

first: Song

last: Han

first: Willard

last: Freeman

first: William

last: Sonntag


title: ChIP-chip from ex-vivo differentiated erythroblasts derived from human primary CD34+ cells

city: Boston

first: Andrew

middle: Jonghan

last: Woo

state: MA

address: 1 Blackfan Circle, Karp Res Bldg

department: Hematology / Oncology

institute: Children's Hospital Boston / Harvard Medical School

type: Genome binding/occupancy profiling by genome tiling array

summary:
The molecular mechanisms underlying erythroid-specific gene regulation remain incompletely understood.  Closely spaced binding sites for GATA, NF-E2/maf and CACCC interacting transcription factors play functionally important roles in globin and other erythroid-specific gene expression.  We and others recently identified the CACCC-binding transcription factor ZBP-89 as a novel GATA-1 and NF-E2/mafK interacting partner.  Here, we examined the role of ZBP-89 in human globin gene regulation and erythroid maturation using a primary CD34+ cell ex vivo differentiation system.  We show that ZBP-89 protein levels rise dramatically during human erythroid differentiation, and that ZBP-89 occupies key cis-regulatory elements within the globin and other erythroid gene loci.  ZBP-89 binding correlates strongly with RNA Pol II occupancy, active histone marks, and high-level gene expression.  ZBP-89 physically associates with the histone acetyltransferases (HATs) p300 and Gcn5/Trrap, and occupies common sites with Gcn5 within the human globin loci.  Lentiviral shRNA knockdown of ZBP-89 results in reduced Gcn5 occupancy, decreased acetylated histone 3 levels, lower globin and erythroid-specific gene expression, and impaired erythroid maturation.  Addition of the HDAC inhibitor valproic acid partially reverses the reduced globin gene expression.  These findings reveal an activating role for ZBP-89 in human globin gene regulation and erythroid differentiation.
Keywords: Antibody ChIP-chip, Human Primary Erythroblasts

overall_design: Genomic targets of Transcription factor ZBP-89 and Histone 3 acetylation signature were identified by ChIP-chip in human primary cells.

first: A

first: J

last: Xu

first: H

last: Huang

middle: B

last: Cantor


title: Mycobacteria-induced anaemia: a molecular approach reveals the involvement of NRAMP1 and lipocalin-2 but not hepcidin

city: Porto

first: Maria

middle: Salome

last: Gomes

address: Rua do Campo Alegre 823

department: IBMC/ICBAS

country: Portugal

institute: Universidad do Porto

summary:
Anaemia is a frequent complication of chronic infectious diseases but the exact mechanisms by which it develops remain to be clarified. In the present work, we used a mouse model of mycobacterial infection to study molecular alterations of iron metabolism.
We show that four weeks after infection with Mycobacterium avium BALB/c mice exhibit a moderate anaemia, which cannot be explained by elevated hepatic hepcidin mRNA expression. Instead, the mice respond with increased mRNA expression of ferroportin (Slc40a1), ceruloplasmin (Cp), hemopexin (Hpx), heme-oxygenase-1 (Hmox1) and lipocalin-2 (Lcn2). Both the anemia and the mRNA expression changes of iron-related genes are largely absent in C.D2 mice which bear a functional allele of the Nramp1 gene. These data suggest that anaemia due to a chronic infection with M. avium develops independently of elevated hepcidin expression and possibly involves ferroportin and/or lipocalin-2.

overall_design: A pool of five mice total RNAs for each condition was used in the experiments. Each two channel chip experiment was done in duplicates with swapped dyes.

first: Pedro

middle: N

last: Rodrigues

first: Sandro

first: João

last: Neves

first: Sandra

last: Gomes-Pereira

first: Margarida

last: Correia-Neves

first: Cláudio

last: Nunes-Alves

first: Jens

last: Stolte

first: Mayka

last: Sanchez

first: Rui

last: Appelberg

first: Martina

middle: U

last: Muckenthaler


title: Effect of folate supplementation on gastric tissue in INS-GAS Helicobacter felis-infected mice

city: NEW YORK

first: TAMAS

last: GONDA

address: 161 FT WASHINGTON

department: MEDICINE

institute: COLUMBIA UNIVERSITY

summary:
Background & Aims: Previous studies have suggested that dietary folic acid (FA) can protect against certain types of cancers.  However, the findings have varied and the mechanisms by which this vitamin exerts chemopreventive effects remain to be clarified.  We examined the effects of FA supplementation on DNA methylation, gene expression and gastric dysplasia in a transgenic mouse model that is etiologically and histologically well matched with human gastric cancers.

Methods: Hypergastrinemic mice (INS-GAS) infected with Helicobacter felis were studied at multiple stages of gastric dysplasia and early cancer, with FA supplementation initiated both at weaning and later in life.  Global DNA methylation was assessed by a methylation-sensitive cytosine incorporation assay, bisulfite pyrosequencing of B1 repetitive elements and immunohistochemistry (IHC) with anti-5-methylcytosine.  We also profiled gene expression in the same tissues.

Results: We found a decrease in global DNA methylation and tissue folate and an increase in serum homocysteine with progression of gastric dysplasia.  FA supplementation prevented this loss of global DNA methylation and markedly reduced gastric dysplasia and mucosal inflammation.  FA protected against the loss of global DNA methylation both in the dysplastic gastric epithelial cells and in gastric stromal myofibroblasts.  In addition, FA supplementation had an anti-inflammatory effect, as indicated by expression profiling and IHC for lymphocyte markers.

Conclusions: We conclude that FA supplementation is chemopreventive in this model of Helicobacter-associated gastric cancer.  The beneficial effect of FA is likely due to its ability to reverse global loss of methylation and suppress inflammation.

overall_design: Study the difference in gene expression between transgenic hypergastrinemic (INS-GAS) mice fed a folate-supplemented diet and a diet with normal folate content.  Because folate had a substantial protective effect, we matched the animals not only by folate status but also by dysplasia score (DYS).  The degree of dysplasia was scored on a 1-4 scale.  True replicates are not included. The first five samples are from folate supplemented animals, and the latter five are from controls on regular chow. The times refer to the number of weeks after infection with H. felis that the animals were switched to a folate-supplemented diet.

first: Tamas

last: Gonda

first: Ben

last: Tycko


title: Salmonella Typhimurium: control vs. T2 toxin treatment

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

institute: Institute of Food Research

summary: Transcriptional profiling of log and stationary phases of S. Typhimurium, comparing untreated controls with T2 toxin-treated samples.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. DT104

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

platform_organism: Salmonella enterica subsp. enterica serovar Enteritidis

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

platform_organism: Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91

overall_design: Each array used labelled cDNA against a common genomic DNA reference. Trplicate arrays were carried out for each of the 4 conditions: untreated log phase, untreated stationary phase, T2 toxin treated log phase and T2 toxin treated stationary phase.

first: Arthur

last: Thompson

first: Elin

last: Verbrugghe


title: P15 Rat Sciatic Nerve ChIP-Chip with NuRD complex components

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary:
The NuRD complex is required for efficient and timely myelination in the peripheral nervous system.  ChIP-chip assays were performed on rat sciatic nerve at P15, a peak timepoint of myelination, for binding of Chd4 to genes involved in regulating myelin formation.
This experiment includes two custom ChIP-chip design incorporating many genes that are dynamically regulated during myelination. The antibodies used in this platform were Chd3/4 (Santa Cruz sc-11378) Chd4 (gift from Paul Wade), Mta2 (Santa Cruz sc-9447), and Nab2 (Santa Cruz sc-22815).

overall_design: Chd4 ChIP samples from experimental and input samples were hybridized.

middle: P

first: Holly

last: Hung


title: Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Benzene vs. Benzoate)

status: Public on Jul 20 2011

city: Amherst

first: Dawn

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

summary: Anaerobic benzene oxidation coupled to the reduction of Fe(III) was studied in Ferroglobus placidus in order to learn more about how such a stable molecule could be metabolized under strict anaerobic conditions.  F. placidus conserved energy to support growth at 85°C in a medium with benzene provided as the sole electron donor and Fe(III) as the sole electron acceptor.  The stoichiometry of benzene loss and Fe(III) reduction, as well as the conversion of [14C]-benzene to [14C]-carbon dioxide, was consistent with complete oxidation of benzene to carbon dioxide with electron transfer to Fe(III).  Benzoate, but not phenol or toluene, accumulated at low levels during benzene metabolism and [14C]-benzoate was produced from [14C]-benzene.  Analysis of gene transcript levels revealed increased expression of genes encoding enzymes for anaerobic benzoate degradation during growth on benzene versus growth on acetate, but genes involved in phenol degradation were not up-regulated during growth on benzene.  A gene for a putative carboxylase that was more highly expressed in benzene- versus benzoate-grown cells was identified.  These results suggest that benzene is carboxylated to benzoate and that phenol is not an important intermediate in the benzene metabolism of F. placidus.  This is the first demonstration of a microorganism in pure culture that can grow on benzene under strict anaerobic conditions and for which there is strong evidence for degradation of benzene via clearly defined anaerobic metabolic pathways.  Thus, F. placidus provides a much needed pure culture model for further studies on the anaerobic activation of benzene in microorganisms.

overall_design: A five-chip study using total RNA recovered from three separate cultures of Ferroglobus placidus DSM 10642 grown with 1 mM  benzene (experimental condition) and two separate cultures of Ferroglobus placidus DSM 10642 grown on 1 mM benzoate (control condition). Each chip measures the expression level of 2,613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Carla

last: Risso

first: Jessica

last: Smith

first: Derek

last: Lovley


title: Comparative Genome Hybridization of Porphyromonas gingivalis strains

first: Emil

last: Kozarov

summary: CGH was used to compare the genomes of a non-invading P. gingivalis strain to the database W83 strain (invader). For hybridization and scanning, TIGR microarrays and protocols were used. The results were independently processed using two different software packages.

overall_design: We used P. gingivalis microarrays in comparative genomics to specifically address the P. gingivalis invasive genotype using invasive and non-invasive phenotypes.

first: Svetlana

last: Dolgilevich

first: Brian

last: Rafferty

first: Darya

last: Luchinskaya


title: Gene Expression Data for Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations

city: Cambridge

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: Patient-specific induced pluripotent stem cells (iPSCs) derived from somatic cells provide a unique tool for the study of human disease in disease relevant cells, as well as a promising source for cell replacement therapies for degenerative diseases. However one of the crucial limitations before realizing the full promise of this “disease in a dish” approach has been the inability to do controlled experiments under genetically defined conditions. This is particularly relevant for disorders with long latency periods, such as Parkinson’s disease (PD), where in vitro phenotypes of patient-derived iPSCs are predicted to be subtle and susceptible to significant epistatic effects of genetic background variations. By combining zinc-finger nuclease (ZFN)-mediated genome editing and iPSC technology we provide a generally applicable solution to this key problem by generating isogenic pairs of disease and control human embryonic stem cells (hESCs) and hiPSCs lines that differ exclusively at a susceptibility variant for PD by modifying a single point mutation (A53T) in the α-synuclein gene. The robust capability to genetically correct disease causing point mutations in patient-derived hiPSCs represents not only a significant progress for basic biomedical research but also a major advancement towards hiPSC-based cell replacement therapies using autologous cells.

overall_design: ZFN-mediated genome edited human iPS cells or ES cells were assayed for gene expression

first: Frank

last: Soldner


title: H4IIE liver cell line ChIP-Chip with Egr1

status: Public on Jul 23 2011

summary:
Egr1 regulates genes involved in cholesterol biosynthesis in liver.  ChIP-chip assays were performed on H4IIE liver cells that were either treated or untreated with insulin for one hour.
This experiment includes a custom ChIP-chip design incorporating many genes that are dynamically regulated by insulin signaling. The Egr1 antibody used was from Santa Cruz sc-189.

overall_design: Egr1 ChIP samples from untreated and 1h insulin treated cells were hybridized.

first: Nolan

last: Gokey


title: Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Benzene vs. Acetate)

overall_design: A six-chip study using total RNA recovered from three separate cultures of Ferroglobus placidus DSM 10642 grown with 1 mM benzene (experimental condition) and three separate cultures of Ferroglobus placidus DSM 10642 grown on 10 mM acetate (control condition).  Each chip measures the expression level of 2,613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.