title: Identification of entertoxigenic Escherichia coli genes transcriptionally altered with the interaction of host cells

status: Public on Nov 26 2012

city: Baltimore

first: David

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

country: USA

institute: University of Maryland School of Medicine

summary: Genes identified in ETEC E24377A after interaction with host cells (Caco-2) after time points of 30 min, 60 min and 120 min.  Both the adherent and non-adherent cells were profiled as well as E24377a grown only in tissue culture media.

platform_organism:
Escherichia coli
Shigella

overall_design: Each time and sample has at least duplicate samples

first: James

last: Fleckenstein


title: Olive (Olea europaea) cv.Chondrolia Chalkidikis: Control vs NaCl-treated

status: Public on Nov 20 2012

city: Chania

first: Maria

middle: E.

last: Manioudaki

address: Makedonias 1

department: Horticultural Genetics and Biotechnology

country: Greece

institute: MAICH

summary: A comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the genotype-dependent differences in the transcriptome response of two olive cultivars, a salt tolerant and a salt sensitive. A 135 day long comparative salinity experiment was conducted using one year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period.   Total RNA was extracted from the root samples after 15, 45 and 90 days of NaCl-treated and un-treated olive trees as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations using a loop design. Hierarchical clustering of differentially expressed transcripts revealed two major, distinct clusters for each cultivar. Despite the limited number of probe set, transcriptional regulatory networks were constructed for the salt-tolerant and salt-sensitive cultivar. The comparison of the salt responsive transcriptional regulatory networks in olive with those reported for Arabidopsis suggests that a tree species might respond in a similar to Arabidopsis way at the transcriptome level under salinity stress.

overall_design: Five experimental time-points were analyzed: 15days stress, 45days stress, 90days stress, 15days post-stress and 45days post-stress. In each timepoint treated and untreated (control) samples were obtained. Dye swap hybridizations and 4 biological replicates were performed for each treatment/timepoint in a loop design experimental setup. Each sample included three spot replicates.

first: Christos

last: Bazakos

first: Ioannis

last: Therios

first: Demetrios

last: Voyiatzis

first: Dimitris

last: Kafetzopoulos

first: Tala

last: Awada

first: Panagiotis

last: Kalaitzis


title: Grape berry: control vs NAA-treated

status: Public on Nov 21 2012

city: Legnaro

first: Alessandro

last: Botton

state: Padova

address: Agripolis - viale dell'università 16

department: Agronomy, Food, Natural resources, Animals and Environment

country: Italy

institute: University of Padova

summary: Transcriptional profiling comparing untreated berries (control) with berries treated with NAA (1-Naphthalene acetic acid, an auxin) at the preveraison stage.

overall_design: Two-condition experiment: control vs. treated. Comparisons were as follows: NAA-treated berries at 60 (days after full bloom (DAFB)) versus untreated berries at 60 DAFB (2 biological replicates, both dye-swapped), NAA-treated berries at 60 DAFB versus NAA-treated berries at 110 DAFB (2 biological replicates, only one dye-swapped), NAA-treated berries at 110 DAFB versus untreated berries at 110 DAFB (2 biological replicates, only one dye-swapped), and NAA-treated berries at 148 DAFB versus untreated berries at 110 DAFB (2 biological replicates, only one dye-swapped).

first: Fiorenza

last: Ziliotto

first: Massimiliano

last: Corso

first: Fabio

middle: M

last: Rizzini

first: Angela

last: Rasori

first: Claudio

last: Bonghi


title: Aspergillus nidulans: Control (Wt) vs. GPCRs mutants (ΔgprB and ΔgprD)

status: Public on Nov 28 2012

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

summary: Transcriptional profiling of A. nidulans comparing the mutant strains ΔgprB and ΔgprD grown on 1% glucose (w/v) in a batch cultivation medium (BCM) at 37°C for 24 and 48h. The main objective was to identifiy genes related to gprB and gprD gene function. The experiment was further validated by real-time PCR and enzymatic assay.

overall_design: Two-condition experiment : A. nidulans strains grown during 24 and 48 h at 37°C in glucose 1% (w/v).


title: gene expression profiling of brain metastatic melanoma cell lines

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

summary: Cerebral metastases occur in a majority of metastatic melanoma patients and are a major cause of mortality. Despite this, there is a poor understanding of the molecules/pathways that lead to the brain-metastatic phenotype. Studies designed to address this deficiency and test novel therapeutic approaches have until recently been slowed by an absence of preclinical models of spontaneous CNS metastatic melanoma disease. To address this, we isolated two variants of the human melanoma cell line WM239 (named 131/4-5B1 and 131/4-5B2) which can metastasize spontaneously to brain parenchyma from an orthotopic primary transplant. We have performed gene expression profiling on both brain metastatic cell lines (131/4-5B1 and 131/4-5B2) and compared to the poorly metastatic parental cell line WM239A and a derived highly metastatic variant 113/6-4L in order to examine the mechanisms that influence the progression of malignant melanoma to a brain-metastatic phenotype.

overall_design: Two-condition experiment, brain metastatic cell lines (131/4-5B1 and 131/4-5B2) and compared to the poorly metastatic parental cell line WM239A and a derived highly metastatic variant 113/6-4L. Biological replicates: 4 independently grown and harvested cell line passages. Two technical replicate per condition (including dye swap).

middle: L

last: Jaramillo

first: William

last: Cruz-Muñoz


title: Expression analysis of miR-139-5p mimic-treated EC109 cells

status: Public on Nov 27 2012

city: Nanjing

first: Ran

last: Liu

address: 87 Dingjiaqiao Street

country: China

institute: Southeast University

summary: Investigation of whole genome gene expression level changes in miR-139-5p mimic-treated EC109 cells, compared to the scrambled negative controls.

overall_design: A four chip study using total RNA recovered from two separate cultures of miR-139-5p mimic-transfected EC109 cells and two separate cultures of scrambled negative control-transfected EC109 cells.  Each chip measures the expression level of 44,049 genes from human esophageal cancer cell EC109 with three 60-mer probe pairs per gene.


title: Transcriptional Responses to Elevated Temperature in Streptococcus agalactiae

status: Public on Nov 18 2012

first: Julie

middle: C

last: Dunning Hotopp

address: 20 Penn St.; HSF-II; S203B

department: Institute for Genomic Sciences

institute: Univeristy of Maryland Baltimore

summary: In the transition from recto-vaginal colonizing organism to invasive pathogen, Streptococcus agalactiae (Group B Streptococcus, GBS) must adapt to changes in host temperature, including elevated temperatures due to host fever.  To identify genes important to the survival of GBS in response to heat stress, transcriptional profiling was performed using DNA microarray analysis, comparing GBS grown at normal temperature (37˚C) to GBS exposed to elevated temperature (42˚C).

overall_design: Two separate RNA samples were extracted for each condition.  Three hybridizations were conducted total.

first: David

last: Klinzing

first: Nadeeza

last: Ishmael

first: Michelle

middle: P

last: Lin

first: Herve

last: Tettelin

first: Karen

last: Puopolo


title: Desulfitobacterium hafniense DCB-2 Gene Expression Differences from Pyruvate Fermentation when Grown with Ferric Citrate, Selenate, Nitrate, or Uranyl Acetate

status: Public on Nov 29 2012

city: East Lansing

first: Christina

last: Harzman

state: MI

address: Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Desulfitobacterium hafniense DCB-2, a halo-respirer and versatile inorganic ion reducer, grows in hazardous waste contaminated environments.  Gene expression changes were determined when the strain was grown in the presence of high concentrations of Fe(+3), Se(+6), U(+6), or NO3(-) as alternative electron acceptors.  (Thesis by Christina L. Harzman at Michigan State University, 2009)

overall_design: RNA was used to directly compare gene expression in control samples of pyruvate fermentation (20 mM) to fermentation in the presence inorganic electron acceptors or respiration-inducing conditions.  The inorganic electron acceptors added to media for fermentation were 1 mM selenate or 0.5 mM uranyl acetate.  The respiration-inducing conditions were 50 mM ferric citrate (20 mM lactate carbon source) or 10 mM nitrate (20 mM lactate carbon source).  Microarray hybridizations were performed with a dye swap and 3 biological replicates for a total of 6 slides per condition for comparison.

first: James

last: Tiedje


title: Effect of glyoxylate pathway deficiency on transcriptome profile of Acetobacter aceti

status: Public on Nov 30 2012

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

department: Department of Biotechnology

country: Japan

institute: The University of Tokyo

summary: Trascriptome profiles in the cells of A. aceti wild-type strain and its isogenic aceA glcB mutant during growth in medium contaning ethanol and glucose was determined by NimbleGen Eukaryotic Expression array (4x72K).

overall_design: Acetobacter aceti NBRC14818 and its isogenic aceA glcB mutant were cultivated in medium containing ethanol and glucose in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.3. The experiment was performed in duplicate independent cultures.

first: Kenta

last: Sakurai

first: Shoko

last: Yamazaki


title: Olive (Olea europaea) cv.Kalamon: Control vs Salt-treated

first: Maria

last: Manioudaki

summary: A transcriptomics approach was used as a tool to unravel gene regulatory network underlying salinity response in a salt-tolerant olive cultivar (cv. Kalamon) by simulating as much as possible olive growing conditions in the field. A 135 day long salinity experiment was conducted using one year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period.   Total RNA was extracted from the root samples after 15, 45 and 90 days of NaCl-treated and un-treated olive trees as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations using a loop design. Hierarchical clustering of differentially expressed transcripts revealed two major, distinct clusters. Despite the limited number of probe set, a transcriptional regulatory networks was constructed for the salt-tolerant cultivar.

overall_design: Five experimental time-points were analyzed: 15days stress, 45days stress, 90days stress, 15days post-stress and 45days post-stress. In each timepoint treated and untreated (control) samples were obtained. Dye swap hybridizations and 4 biological replicates were performed for each treatment/timepoint in a loop design experimental setup. Low-quality arrays were not included in the data analysis (36 arrays/samples submitted). Each sample included three spot replicates.

first: Christos

last: Bazakos

first: Ioannis

last: Therios

first: Demetrios

last: Voyiatzis

first: Dimitris

last: Kafetzopoulos

first: Tala

last: Awada

first: Panagiotis

last: Kalaitzis


title: Francisella Expression Microarray Analysis

city: San Antonio

first: Xhavit

last: Zogaj

address: One UTSA Circle

department: Biology

institute: UTSA

summary:
Francisella tularensis is a Gram-negative bacterium that is highly virulent in humans, causing the disease tularemia. F. novicida is closely related to F. tularensis and exhibits high virulence in mice, but is avirulent in healthy humans. A F. novicida-specific gene cluster (FTN0451-FTN0456) encodes two proteins with diguanylate cyclase (DGC) and phosphodiesterase (PDE) domains that modulate synthesis and degradation of cyclic di-GMP (cdGMP). No DGC or PDE containing proteins are present in the F. tularensis genome. F. novicida strains lacking either the two DGC/PDE genes cdgA and cdgB or the entire gene cluster (KKF457) are defective for biofilm formation. In addition, expression of CdgB or a heterologous DGC in KKF457 stimulated F. novicida biofilms, even in a strain lacking the biofilm regulator QseB. Genetic evidence suggests that CdgA is predominantly a PDE, while CdgB is predominantly a DGC.
The F. novicida qseB strain has reduced cdgA and cdgB transcript levels, demonstrating a F. novicida biofilm signaling cascade that controls cdGMP levels. Interestingly, KKF457 with elevated cdGMP levels exhibited a decrease in intramacrophage replication and virulence in mice, as well as increased growth yield and biofilm formation in vitro. Microarray analyses revealed that cdGMP stimulated the transcription of a chitinase (ChiB) known to contribute to biofilm formation. Our results indicate that elevated cdGMP in F. novicida stimulates biofilm formation and inhibits virulence. We suggest that differences in human virulence between F. novicida and F. tularensis may be due in part to the absence of cdGMP signaling in F. tularensis.

overall_design: A whole genome NibleGen microarray was developed for multiple Francisella subspecies, using shared probes for common genes as well as unique probes for subspecies-specific genes. Included were probes representing the F. novicida U112 genome, with a maximum of 6 probes/gene. RNA was isolated from bacteria and purified as described above. The double-strand cDNA was generated and labeled with Cy3 according to the NimbleGen Gene Expression Array protocol (www.nimblegen.com), using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and the DNA Labeling Kit (NimbleGen). Microarray results were analyzed using the ArrayStar software (DNASTAR).

first: Geoff

last: Wyatt

first: Karl

middle: E

last: Klose


title: LiaR Transcriptome in Streptococcus agalactiae

first: Julie

last: Dunning Hotopp

summary: Streptococcus agalactiae (Group B Streptococcus, GBS) is a leading cause of early-onset neonatal bacterial infection.  Evasion of innate immune defenses is critical to neonatal GBS disease pathogenesis.  Effectors of the innate immune system such as antimicrobial peptides, as well as numerous antibiotics, target the peptidoglycan layer of the gram positive bacterial cell wall.  The intramembrane-sensing histidine kinase class of two-component regulatory systems has recently been identified as important to the gram-positive response to cell wall stress.  We identified and characterized the GBS homolog of LiaR, the response regulator component of the LiaFSR system and constructed site-directed, non-polar deletion mutations in the regulator gene liaR.  GBS LiaR deletion mutant strains are more susceptible to cell wall active antibiotics (vancomycin and bacitracin) as well as antimicrobial peptides (colistin, nisin and the human cathelicidin LL-37) compared to isogenic wild-type GBS.  LiaR mutant GBS are significantly attenuated in mouse models of both GBS sepsis and GBS pneumonia.  To determine the genes regulated by LiaR that account for these defects, transcriptional profiling was performed using DNA microarray analysis, comparing wild-type GBS to LiaR mutant GBS under non-stressed conditions.

overall_design: Two separate RNA samples were extracted for each condition.  One flip-dye replicate (2 hybridizations) was obtained for each pair of RNA samples for 4 hybridizations total.

first: David

last: Klinzing

first: Gilles

middle: R

last: Bolduc

first: Nadeeza

last: Ishmael

first: Kelly

last: Shields

first: Lawrence

last: Madoff

first: Herve

last: Tettelin


title: Expression data from bone marrow derived granulocyte monocyte precursors (GMPs) from wt -, Gfi1 knock-out -, human-Gfi1-SNP36N knock in and human wt-Gfi1 knock in mice

status: Public on Nov 22 2012

city: Essen

first: Cyrus

last: Khandanpour

address: Hufelandstr. 55

department: Hematology

country: Germany

institute: University Hospital Essen

summary:
The incidence of cancer is not only influenced by exposure to environmental factors such as toxic substances and chemotherapy, but is also a result of individual predispositions. Single Nucleotide Polymorphisms (SNPs) represent one such individual predisposition to cancer1. Gfi136N is a SNP in the coding region of the gene “Growth factor independence 1 (Gfi1)” predisposing to development of Acute myeloid leukemia (AML). However, the mechanisms how this polymorphism is associated with AML are unknown. Here we present a mouse model in which the presence of Gfi136N leads to altered epigenetic modifications in the myeloid progenitor fraction “Granulocytic Monocytic Progenitor (GMP)” and demonstrates how this might predispose to AML.  Presence of Gfi136N leads to a different epigenetic programming of the GMPs resulting in higher levels of the leukemogenic transcription factor Hoxa9. To our knowledge, this is the first mouse model of a SNP leading to epigenetic changes. Thus, SNPs not only result in an altered structure or expression level of certain proteins but here we show that SNPs might also lead to different cancer related epigenetic modifications.
We used microarrays to detail the changes in the program of gene expression of GMPs induced by the knock in of human Gfi1 variants in the mouse Gfi1 locus

overall_design: Bone marrow derived granulocyte monocyte precursors (GMPs) from wt.-,Gfi1 knock-out.-, human Gfi1-knock in and human Gfi1-SNP36N knock in mice were collected by fluorescence activated cell sorting (FACS) for total RNA extraction and gene expression analysis on affymetrix mouse Gene 1.0 ST arrays. We aimed to identify differentially regulated target genes of the human Gfi1-SNP36N variant in a mouse model system which mit contribute to the development of acute myeloid leukemia (AML).

first: Joseph

last: Krongold

first: Lothar

last: Vassen

first: Riyan

last: Chen

first: Bert

last: van der Reijden

first: Joop

last: Jansen

first: Marie-Claude

last: Gaudreau

first: Justine

middle: K

last: Peeters

first: Bob

last: Lowenberg

first: Chandrashekhar

middle: V

last: Patel

first: Ulrich

last: Dührsen

first: Tarik

last: Moroy


city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

summary: Comparison of Bacillus subtilis wild type and cshA mutant at exponential versus stationary phase. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can  be found in the submitted paper.

overall_design: Bacillus subtilis 168 wild type and its cshA derivative strain were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationary phase (OD600 ~2.2-2.4).  For both time points, 4 biological replicates were used and 2 were mixed after cDNA labeling, resulting 2 slides for both exponential and stationary phase. Dye swaps are included in both experiments.

first: Martin

last: Lehnik

first: Oscar

last: Kuipers

first: Jorg

last: Stulke


title: Differentially expressed miRNAs in MDA-MB-231 over-expressing GATA3

city: San Francisco

first: Jonathan

last: Chou

address: 513 Parnassus Ave, Box 0452, HSW1301

department: Anatomy

institute: Univ of California, San Francisco

summary: To determine the differentially expressed miRNAs in MDA-MB-231-GATA3 cells vs. MDA-MB-231-Control cells

overall_design: Pooled polyclonal cells from MDA-MB-231 breast cancer cells +/- GATA3 over-expression were analyzed for miRNA expression

first: Zena

last: Werb


title: Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis

first: Joseph

middle: G.

last: Gall

address: 3520 San Martin Drive

department: Department of Embryology

institute: Carnegie Institution for Science

summary: To compare nuclear and cytoplasmic RNA from a single cell type, free of cross-contamination, we studied the oocyte of the frog Xenopus tropicalis, a giant cell with an equally giant nucleus. We isolated RNA from manually dissected nuclei and cytoplasm of mature oocytes and subjected it to deep sequencing. Cytoplasmic mRNA 10 consisted primarily of spliced exons derived from ~6700 annotated genes. Nearly all of these genes were represented in the nucleus by intronic sequences. However, unspliced nascent transcripts were not detected. Inhibition of transcription or splicing for 1–2 d had little or no effect on the abundance of nuclear intronic sequences, demonstrating that they are unusually stable. RT–PCR analysis showed that these stable intronic sequences are transcribed from the coding strand and that a given intron can be processed into more than one 15 molecule. Stable intronic sequence RNA (sisRNA) from the oocyte nucleus constitutes a new class of noncoding RNA. sisRNA is detectable by RT–PCR in samples of total RNA from embryos up to the mid-blastula stage, when zygotic transcription begins. Storage of sisRNA in the oocyte nucleus and its transmission to the developing embryo suggest that it may play important regulatory roles during oogenesis and/or early embryogenesis.

overall_design: The individual germinal vesicle (GV) samples' log2 signals were compared pairwise with those from enucleated oocytes.

first: Eugene

middle: J

last: Gardner

first: Zehra

middle: F

last: Nizami

first: C

last: Talbot Jr

middle: G


title: Comparison of microarray platforms for measuring differential microRNA expression (Exiqon data)

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary:
Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it  does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens.  We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues.
The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples.

overall_design: Nine paired tumor/normal colon tissues on Exiqon miRCURY LNA microRNA Array

first: Maurizio

last: Callari


title: Systems analysis of the Merck Ad5/HIV vaccine reveals robust induction of a core innate immune gene network: in vivo analysis

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

summary:
Here we applied a systems approach to define human innate immune signatures following MRKAd5/HIV immunization and to analyze the effects of pre-existing Ad5 immunity.
We defined the global early immune response to MRKAd5/HIV by profiling the PBMC transcriptomes from seven Ad5Neg individuals pre- and post-vaccination in vivo.
Since the Step Study results suggested a deleterious effect of pre-existing Ad5 nAb on vaccine immunogenicity, we examined the vaccine-induced transcriptional responses from two Ad5Med and one Ad5Low individual

overall_design:
50 total samples were analyzed.   This includes 5 time points post vaccination with MRKAd5/HIV for 10 independent human subjects.  The time points were 0hr, 6hrs, 24hrs, 72hrs, and 168hrs.
Seven of the subjects did not have pre-existing neutralizing antibodies to the vaccine vector (Ad5Neg).  One subject had low level pre-existing neutralizing antibodies to the vaccine vector (Ad5Low).  Two subjects had moderate level pre-existing neutralizing antibodies to the vaccine vector (Ad5Low).

first: Erica

last: Andersen-Nissen

first: M

last: McElrath

first: Alan

last: Aderem


title: Transcriptome changes in Streptococcus agalactiae due to deletion of both the CiaR and LiaR Transcriptional Regulators

first: Julie

last: Dunning Hotopp

summary: The CiaRH and LiaFSR two-component regulatory systems in Streptococcus agalactiae (Group B Streptococcus, GBS) are essential mediators of the organism s response to biologically important sources of environmental stress, and positive regulators of GBS virulence. Transcriptional profiling of CiaR mutant GBS and LiaR mutant GBS reveals that LiaR is positively-regulated by CiaR, and the individual mutant transcriptomes share a number of commonly-regulated genes.  To determine the GBS response to loss of both of these key regulatory systems, we constructed a GBS mutant strain with non-polar deletions in both ciaR and liaR, and performed transcriptional profiling using DNA microarray analysis, comparing wild-type GBS to CiaR/LiaR double mutant GBS under non-stressed conditions.

first: David

last: Klinzing

first: Nadeeza

last: Ishmael

first: Herve

last: Tettelin

first: Karen

last: Puopolo


title: Effect of Supplementing Linseed in the Transition Period on Mammary Gland Tissue of dairy Cows

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

country: France

institute: INRA

summary:
The aim of this study was to determine the effects of linseed dietary supplementation on gene expression in the mammary gland of grazing dairy cows.
Milk composition and gene expression in the mammary gland tissue were evaluated in dairy cows supplemented with linseed. The linseed supplementation improves the health and nutrition quality aspects of dairy milk, but also affects the gene networks expression signature associated with cellular growth and proliferation, cell-death, signalling, nutrient metabolism, and immune response, and in turn, the mammary gland integrity and health.

overall_design: The experiment was carried out in a complete randomized blocked designed structure comprising 14 Holstein-Friesian cows (6 second parity, 2 third parity and 6 older cows), selected from a 550-cow herd. Cows were paired in 7 blocks on the basis of similarity in parity (second parity, third parity and older cows), expected date of calving, and milk performance in the previous lactation (in order of priority). Cows within each block were randomly allocated to one of two treatment groups, “Omega” or “Control”. The dietary Omega treatment consisted of a basal diet supplemented with a concentrate-mixture including linseed on a dry matter (DM) basis, whereas cows in treatment group Control were supplemented with a concentrate mixture without linseed. Linseed was chosen because it is rich in c9,c12,c15-18:3 (ALA). Concentrate mixtures were fed with a concentrate dispenser. Experimental treatments started 3 weeks before the expected calving date (wk -3) and lasted until 6 weeks after calving (wk 6).

first: N

first: R

last: Zom

first: A

last: Widjaja

first: P

last: Van Wikselaar

first: E

last: Weurding

last: Goselink

first: J

last: Van Baal

first: Mari

last: Smits

last: Van Vuuren


title: CiaR Transcriptome in Streptococcus agalactiae

summary: Regulation of gene expression in response to variable and often adverse environmental conditions is an essential component of microbial pathogenesis.  We identified the two-component regulatory system CiaRH in a screen for genes essential for the survival of Streptococcus agalactiae (Group B Streptococcus, GBS) on exposure to in vitro models of environmental stress.  We constructed site-directed, non-polar deletion mutations in the regulator gene ciaR and compared the growth of CiaR mutant GBS to wild-type GBS under stressed conditions.  CiaR mutant GBS are more sensitive than wild-type GBS to elevated temperature, low pH, chemical mutagens and ultraviolet light; the mutants are also more sensitive to cell-wall active antibiotics and antimicrobial peptides.  CiaR mutant strains are markedly attenuated in a mouse model of GBS sepsis.  To determine the genes regulated by CiaR that account for these defects, transcriptional profiling was performed using DNA microarray analysis, comparing wild-type GBS to CiaR mutant GBS under non-stressed conditions.

sample_organism:
Streptococcus agalactiae
Streptococcus agalactiae A909

first: Michelle

last: Lin


title: Systems analysis of the Merck Ad5/HIV vaccine reveals robust induction of a core innate immune gene network: in vitro analysis

first: Daniel

last: Zak

summary:
Here we applied a systems approach to define human innate immune signatures following MRKAd5/HIV immunization and to analyze the effects of pre-existing Ad5 immunity.
To determine whether vaccine-induced changes could be ascribed to cell-intrinsic responses rather than cell population fluxes, fresh PBMC from independent Ad5Neg donors were stimulated in vitro with MRKAd5 vector lacking HIV-1 transgenes (MRKAd5).

overall_design:
22 total samples were analyzed.  14 of these are from in vivo vaccination of seven Ad5 seronegative subjects at two time points (0hr and 24hrs).
8 of these are from 24hr in vitro stimulation of PBMCs from four independent Ad5 seronegative donors with MRKAd5 empty vector or GTS buffer (Mock) at 20,000 viral particles per cell.

first: Erica

last: Andersen-Nissen

last: McElrath


title: Pig Longissimus muscle: comparison between Basque and Large White breeds

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

summary: Transcriptional profiling of pig skeletal muscle comparing two divergent breeds: Large white (LW, conventional) and Basque (B, local, indigeneous).

overall_design: Two-condition experiment, LW vs. B muscles. Biological replicates: 20 B and 20 LW. One replicate per array.

first: Marie

last: Damon

first: Joanna

last: Wyszynska-Koko

first: Bénédicte

last: Lebret


title: Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (Affymetrix)

status: Public on Nov 16 2012

city: Maastricht

first: Stan

last: Gaj

state: Limburg

address: Universiteitssingel 50

department: Department of Toxicogenomics

country: Netherlands

institute: Maastricht University

summary: Whole-genome transcriptome measurements are pivotal for characterizing carcinogenic mechanisms of chemicals and predicting toxic classes, such as genotoxicity, from in vitro and in vivo assays. DNA microarrays have evolved as the gold standard for this purpose. In recent years deep sequencing technologies have been developed that hold the promise of measuring the transcriptome with RNA-seq in a more accurate and unbiased manner than microarrays. So far, however, few applications have been published that assess the performance of RNA-seq within a toxicogenomics context. Here, we applied RNA-seq for the characterization of the in vitro transcriptomic responses in HepG2 cells upon exposure to benzo[a]pyrene (BaP), a well-known DNA damaging carcinogen. We demonstrate the performance of RNA-seq with respect to the identification of differentially expressed genes and associated pathways, in comparison with microarray technology. RNA-seq data generates more complete and thus accurate data on differentially expressed genes and affected pathways than microarrays. Additionally, we highlight the potential of RNA-seq for characterizing mechanisms related to alternative splicing and thereby gathering new information. Exposure to BaP alters the isoform distribution for many genes, including regulators of cell death and DNA repair such as TP53, BCL2 and XPA, which are relevant for genotoxic responses. Finally, we demonstrate that RNA-seq enables to investigate allele-specific gene expression, although no changes for that could be observed. Our results provide evidence that RNA-seq is a powerful tool for toxicology which, compared to microarrays, is capable of adding valuable information at the transcriptome level for characterizing toxic effects caused by chemicals.

overall_design: Examination of 2 biological replicates at 2 different timepoints

first: Joost

last: vanDelft

first: Jos

last: Kleinjans


title: Comparison of microarray platforms for measuring differential microRNA expression (Miltenyi data)

first: Loris

last: De Cecco

overall_design: Nine paired tumor/normal colon tissues on Miltenyi miRXplore Microarray.

first: Maurizio

last: Callari


title: The nsrR regulon in Salmonella Typhimurium 14028s

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: In this study, we have defined the NsrR regulon in Salmonella enterica sv. Typhimurium 14028s using a transcriptional microarray. Wild-type and nsrR mutant S. Typhimurium were grown aerobically to early log-phase (OD600~0.5) at 37C in LB medium. Total RNA was isolated from three independent cultures of both strains and interrogated on a PCR product array representing almost all ORFs.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Three biological replicates of wt and nsrR mutant total RNAs, Cy3 and Cy5 dye swapped, were hybridized onto six PCR product arrays in two channels.

first: Steffen

last: Porwollik

first: Joyce

last: Karlinsey

first: Iel-Soo

last: Bang


title: Profiling of differentially expressed genes in sheep T lymphocytes response to Haemonchus contortus infection

city: Hangzhou

first: Aifang

last: Du

state: Zhejiang

address: Yuhangtang Road 866

department: College of Animal Sciences, Zhejiang University

institute: Institute of Preventive Veterinary Medicine

summary: Once Haemonchus contortus infects sheep it receives a series of host attacks, especially those relating to the infected animal’s T lymphocytes immune response. To obtain a systematic genome-wide profiling of the T lymphocyte genes involved, microarrays were used to compare gene expression between 0 days post infection (dpi), 3-5 dpi, 25-30 dpi and 60dpi in infected sheep. In this 853, 242 and 42 differentially expressed genes were acquired in the 3d vs. 0d comparison, the 30d vs. 0d comparison and the 60d vs. 0d comparison, respectively. Gene Ontology and pathway analysis indicated that modulated genes including SUGT1, FCER1G, CD23, IL-13 and galectin-14, were mostly associated with cellular homeostasis maintaining and immune response.

overall_design: Haemonchus contortus infection induced gene expression in sheep T lymphocytes was measured at 0, 3, 30 and 60 days post infection. Four time-series experiments were performed at each sheep (2#, 3# and 5#).

first: Yi

last: Yang


title: cDNA microarray assay of lymph node biopsies diagnosed as lymphoma or as reactive tissue

city: Darlinghurst

first: David

last: Ma

state: NSW

address: L8 Lowy Packer Building, 405 Liverpool St

department: Haematology research

country: Australia

institute: St Vincent's Hospital

summary:
Gene expression profiling of biopsied human lymph node (LN) tissue comparing each patient sample against mobilised peripheral blood stem cells (PBSC), the reference channel
Evaluate whether gene expression microarray can diagnose lymph node biopsies as reactive or as one of three main types of lymphoma: classical Hodgkin’s lymphoma (cHL), diffuse large B cell lymphoma (DLBCL) or follicular lymphoma (FL).

overall_design: Two condition experiment, LN vs mobilised PBSC, 116 cases assayed, 1 replicate per array

middle: D


title: Interferon signaling during early experimental malaria infection

status: Public on Nov 19 2012

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary: Microarray profiling of whole blood of immunodeficient mouse strains at 24h after infection with Plasmodium chabaudi.

overall_design: Multiple independent replicates collected for each knockout.  RNA isolated and amplified.  Hybridized as two-color experiment against a common pooled reference.

first: Charles

first: Christopher

middle: S

last: Nelson

first: Baidong

last: Hou

first: Tony

last: DeFranco

first: Joseph

last: DeRisi


title: Time course of grapevine bud development

status: Public on Nov 17 2012

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: Buds were collected at equivalent branch positions and always at the same time of the day. Samples corresponding to May (MAY), June (JUN), July (JUL), September (SEP), November (NOV), January (JAN), March (MAR) and April (APR) buds were analyzed.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Jose Diaz-Riquelme.  The equivalent experiment is VV36 at PLEXdb.]

overall_design: time: MAY(3-replications);  time: JUNE(3-replications);  time: JULY(3-replications);  time: SEPTEMBER(3-replications);  time: NOVEMBER(3-replications);  time: JANUARY(3-replications);  time: MARCH(3-replications);  time: APRIL(3-replications)

first: Jose

last: Diaz-Riquelme

first: JoseM

last: Martinez-Zapater


title: Depth Distribution of Ammonia Oxidation Rates and Ammonia-Oxidizer Community Composition in the Sargasso Sea

status: Public on Nov 15 2012

city: Boston

first: Silvia

last: Newell

state: Massachusetts

address: 675 Commonwealth Ave.

institute: Boston University

summary: Ammonia oxidizer community structure were examined in a depth profile from 20 to 2000 m at the Bermuda Atlantic Time-series Study using a functional gene microarray to look at amoA diversity

sample_organism:
synthetic construct
uncultured ammonia-oxidizing archaeon

overall_design: Two color array (cy3 and cy5): the universal standard 20 bp oligo (fluoresced with cy5) is printed to the slide with a 70-mer. Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer will bind to it.  Signal is the cy3/cy5. Two replicate arrays were run on duplicate targets.

first: Bess

last: Ward

first: Sarah

last: Fawcett


title: ccpA Chromatin immunoprecipitation on chip of JIR8094 (CD630E) WT strain and a ccpA mutant after 6h of growth in TY

status: Public on Nov 13 2012

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

type: Genome binding/occupancy profiling by array

summary: Comparison of ccpA Chromatine immunoprecipitation on chip using 2 strains : JIR8094 (CD630E) wild type strain and a ccpA mutant after 6h of growth in TYG. This experimental procedure was designed to investigate the consensus binding site, CRE, of pleiotropic regulator ccpA.

overall_design: Two-conditions experiments, JIR8094 (CD630E) strain 6h vs ccpA mutant 6h, 3 biological replicates for each condition

first: Emmanuelle

last: Courtois

first: Marc

last: Monot


title: Heterologous hybridization to an oligonucleotide microarray monitors differential gene expression in Pinus radiata exposed to long-term Ethephon exposure

city: Rotorua

middle: Gogo

last: Dubouzet

address: 49 Sala St

department: Biotransformation

country: New Zealand

institute: Scion

summary:
Comparison of transcriptomes from bark, developing xylem and xylem of P. radiata saplings exposed to 0 or 1mg of Ethephon in lanolin for 1 or 8 weeks
We developed an oligonucleotide microarray using sequences (mostly from Pinus taeda) from public sequence databases. These sequences were reconstituted into a non-redundant database by CAP3 assembly and used as templates for automated design of 60-mer oligonucleotide probes through eArray, Agilent’s online facility. The microarray slides, manufactured by Agilent, were used to monitor gene expression in an Ethephon-induction experiment. Ethephon was dispersed in lanolin paste and applied in a 3 cm band near the base of the stem of 2-year old Pinus radiata saplings. RNA was extracted from bark, cambial region, also known as “developing xylem”, and xylem tissues exposed for 1 or 8 weeks to Ethephon. The transcriptomes from these extracts were compared by hybridization onto the All-Pinus microarray slides. Statistically significant differentially expressed genes identified by limma (Linear Models for Microarray Data) were subsequently analysed by singular enrichment analysis through the Database for Annotation, Visualization and Integrated Discovery (DAVID) portal. Results revealed that bark, cambial region and xylem generate mostly mutually exclusive cohorts of genes and Gene Ontology (GO) classes. Ethephon induction led to the upregulation of xylem genes related to the metabolism of phenylpropanoids and flavonoids and to defence responses, specifically, fungal/insect attack and oxidative stress. Independent validation of the microarray data for five genes was obtained by quantitative RT-PCR. The results are also interpreted in reference to gross and microscopic morphological changes. These results confirm the utility of the All-Pinus microarray for transcriptomic research in P. radiata.

overall_design: Series of 2-color, 2 condition experiments in 12  180k arrays. Main comparison is within tissues exposed to 0 [control] or 1 mg Ethephon. 2nd level of comparison is between tissues [bark, xylem scraping, xylem]. Third level of comparison is between time [ 1 or 8 week exposure]. One slide is hybridized with cRNA generated from control and treated tissues with the same duration of exposure to Ethephon. Two biological replicates [each biological rep is a 2 y old cutting propagated clone] for treated plants whilst control consists of RNA pooled, in equal proportions [estimated by UV absorbance], from 2 untreated  biological replicates.]. Dyes used for each sample are indicated in sample description.

first: Lloyd

last: Donaldson

first: Michael

middle: A

last: Black

first: Vincent

last: Liu

first: Gareth

last: Lloyd-Jones


title: Metabolic responses of the model archaeon Halobacterium sp. NRC-1 to oxygen limitation

status: Public on Nov 06 2012

city: Baltimore

first: Priya

last: DasSarma

address: 701 East Pratt Street, Suite 236

department: Microbiology

institute: UMB

summary: As part of a comprehensive post-genomic investigation of the model archaeon Halobacterium sp. NRC-1, we used whole genome DNA microarrays to compare transcriptional profiles of cells grown anaerobically via arginine fermentation versus cells either respiring aerobically in the presence of oxygen or anaerobically using trimethylamine N-oxide (TMAO) as a terminal electron acceptor.

overall_design: In the study presented here, a consecutively performed series of experiments were performed to examine the effects of regulator deletions (dmsR, bat) and oxygen limitations of Haloarchaeal cells. Microarrays were used to acquire expression profiles of a total of 2484 genes, leading to the successful identification of affected genes.

first: Shiladitya


title: Immune response biomarker profiling of serum from prostate cancer patients treated with anti-CTLA-4 immunotherapy.

status: Public on Nov 05 2012

first: Serena

last: Kwek

address: 513 Parnassus Ave.

institute: UCSF

summary: Anti-CTLA-4 induced antibody responses to antigens in prostate cancer patients.

overall_design: Pre-treatment and post-treatment sera from 5 clinical responders and 6 clinical non-responders were used to hybridize protein arrays.

first: Lawrence

last: Fong


title: Microarray analysis of Haemophilus parasuis SH0165 genomics induced by tilmicosin

status: Public on Nov 10 2012

city: Wuhan

first: Liu

last: yingyu

address: Hongshan district, No.1

institute: Huazhong agricultural university

summary: To gain an extensive understanding of the molecular mechanisms of tilmicosin, we can begin by understanding the different regulated responses of bacteria to tilmicosin and studying the physiological activity of bacteria. In this study, we used microarray technology to analyze the variation of the H. parasuis SH0165 transcriptional profile in response to inhibitory and sub-inhibitory concentrations of tilmicosin. Our analysis to identify several genes whose system could be involved in the protection from antibiotic stress targeting the ribosome 50 subunit and help to confer the basal level of H. parasuis responses to antibacterial drugs, such as heat shock protein, ribosome and ribosome related transcription genes, the cell wall biogenesis genes. Quantitative RT-PCR was used to validate the differential expression of fifteen selected genes.

overall_design: H. parasuis SH0165 was induced by 0.25µg/ml tilmicosin at OD600 >0.3 (16 h). The 8µg/ml tilmicosin treatment was 50 mins at OD600 >0.3 (12 h). The H. parasuis SH0165 control group was normal culture with no tilmicosin at OD600 >0.3 (12 h). Three independent experiments were performed on each group using a different sample for each experiment.

first: Yingyu


title: Mechanism of cell death induced by saporin

status: Public on Nov 09 2012

city: Los Angeles

first: Manuel

last: Penichet

department: Department of Surgery

institute: University of California, Los Angeles

summary:
Insights into the mechanism of cell death induced by saporin delivered into cancer cells by an antibody fusion protein targeting the transferrin receptor 1
These studies detail transcriptional changes induced in cancer cells by the complex of saporin (b-SO6) and the antibody fusion protein ch128.1Av. Delivery of saporin into cancer cells by ch128.1Av, induces a transcriptional response consistent with oxidative stress and DNA damage, a response that is not observed with ch128.1Av alone.

overall_design: Time course, after delivery of saporin into cells by ch128.1Av

middle: L

first: Tracy

last: Daniels


city: Bristol

first: Anthony

last: Dallosso

address: University Walk

department: School of Cellular & Molecular Medicine

country: United Kingdom

institute: University of Bristol

type: Genome binding/occupancy profiling by genome tiling array

summary: The Wilms' tumour 1 transcription factor regulates epigenetic states via DNA methyltransferase 3A.

overall_design: The data consists of two Nimblegen promoter/CpG island microarrays hybridized with MCIP DNA immunoprecipitated from either a HEK293-derived cell line expressing a heterologous WT1 cDNA (W210) or a control cell line containing the expression vector (IP100), both hybridized against input DNA.


title: Analysis of gene content among Group II Clostridium botulinum strains

status: Public on Nov 08 2012

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

summary:
The purpose of this study was to compare the gene content of several group II C. botulinum strains to determine the utility of DNA microarrays for subtyping this organism.
Group II type B, E, and F C. botulinum strains were compared in a study to examine the gene content of a unique type E strain (CDC66177).

overall_design: One replicate of genomic DNA isolated from 16 type E strains, 4 type B strains, and 2 type F strains were examined.

first: Matthew

last: Lautenschlager

first: Suzanne

last: Kalb

first: Laura

middle: I

last: deJong

last: Frace

first: Carolina

last: Luquez

first: John

last: Barr

first: Rafael

last: Fernandez

first: Susan

last: Maslanka


title: Effects of manR disruption and overexpression on Aspergillus oryzae gene expression

city: Noda City

first: Masahiro

last: Ogawa

state: Chiba

address: 399 Noda

institute: Noda Institute for Scientific Research

summary: Fungal endo-β-mannanases (β-mannanases) are widely used as industrial enzymes; however, no transcriptional regulator of β-mannanases has been identified in fungi or other eukaryotic cells to date. To identify a transcriptional regulator of β-mannanases in Aspergillus oryzae, a gene-disruptant library of transcriptional regulators was screened for mutants exhibiting reduced β-mannanase activity by using konjac glucomannan as the substrate, and ManR, a Zn(II)2Cys6 type DNA binding protein was identified. Moreover, a manR-overexpressing strain showed significantly increased β-mannanase activity. DNA microarray analysis of the manR-disruptant strain and the manR-overexpressing strain further indicated that when konjac glucomannan is used as the carbon source, ManR positively regulates the gene expression of not only β-mannanase, but also the enzymes involved in the degradation of galactomannans and glucomannans such as α-galactosidase, β-mannosidase, acetylmannan esterase, and β-glucosidase. Therefore, we conclude that ManR is a positive regulator of the β-mannan utilization system in A. oryzae.

overall_design: manR disruptant, manR-overexpressing strain and A. oryzae RkuptrP2-1∆AF/P (derivative of A. oryzae RIB40) were cultivated in  minimal medium containing 1% konjac glucomannan as the sole carbon source. After 6 h cultivation, total RNAs from the mycelia were extracted, and DNA microarray analysis was carried out. The analysis of manR disruptant was conducted with 4 biological replications,  the analysis of manR overexpressing strain was conducted with 3 biological replications.

first: Tetsuo

last: Kobayashi

first: Yasuji

last: Koyama


title: A model system for assessing the ability of exon microarray to detect genes specific for malignant B-cells

status: Public on Nov 07 2012

city: Aalborg

first: Maria

middle: Bro

last: Kloster

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg Hospital

summary:
The purpose of this study was to develop a quantification method that can be used to assess the ability of exon microarray to detect malignant B-cell transcripts.
The data support that tumour cell concentration is an important variable with fundamental impact on gene expression pattern.

overall_design: We analysed eight serial dilutions of the malignant B-cell line, OCI-Ly8, into the embryonic kidney cell line, HEK293, by Affymetrix GeneChip Human Exon 1.0 ST Platform. Array data was processed by Affymetrix Exon Microarry Computional Tool. No technical replicates were performed.

middle: B

first: Anders

middle: E

last: Bilgrau

last: Rodrigo-Domingo

first: Kim

last: Bergkvist

first: Alexander

last: Schmitz

first: Mads

last: Sønderkær

first: Julie

last: Bødker

first: Steffen

last: Falgreen

first: Mette

last: Nyegaard

first: Hans

last: Johnsen

first: Kåre

last: Nielsen

first: Karen

last: Dybkaer

first: Martin

last: Bøgsted


title: Profiling of transcripts in developing seeds of common bean (Phaseolus vulgaris) lines differing in major storage proteins

city: London

first: Frederic

last: Marsolais

address: 1391 Sandford Street

institute: Southern Crop Protection & Food Research Centre

summary: To understand the molecular basis for differences of common bean wild-type and mutant in sulphur amino acid content, transcripts were profiled at four developmental stages of seeds from wild-type SARC1 and major seed storage protein-deficient line SMARC1N-PN1 using a CustomArray 90K array. Microarray data confirmed that transcripts of storage and sulphur-rich proteins and sulphur-metabolism related genes were differentially expressed between the lines.

overall_design: The common bean (Phaseolus vulgaris) mutant line, SMARC1N-PN1 and its wild type, SARC1 used in the  microarray  experiment were grown in the field in London, ON, in 2009. Four developmental stages of seeds, based on fresh seed weight, were harvested. The stages of seeds used are Stage IV – cotyledon, 25 mg seed weight; Stage V – cotyledon, 50 mg seed weight; Stage VI – maturation, 150 mg seed weight, corresponding to the most active phase of reserve accumulation; and Stage VIII – maturation, 380 mg seed weight, corresponding to the onset of desiccation, were harvested for total RNA extraction. Four biological replicates for  Stage IV and V and 3 biological replicates for Stage VI and VIII.

first: Dengqun

last: Liao

first: Frédéric


title: BSO-treated blastocysts vs CTL-treated blastocysts

status: Public on Nov 14 2012

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

summary: In order to understand how in vitro culture affects embryonic quality, we analyzed survival and global gene expression in bovine blastocysts after exposure to increased oxidative stress conditions of IVC. A pro-oxidant agents that act intra-cellularly by inhibiting GSH synthesis (0.4 mM buthionine sulfoximine [BSO]) was added from days 3 to 7, and transcriptomic analysis was then performed in resulting blastocysts. Precisely, after in vitro maturation and fertilization, bovine zygotes were culture in vitro in normal condition, then at day 3, embryos were allocated into culture in control or supplemented with BSO (0.4 mM) until day 7. At this time, blastocysts were harvested and analyzed. Our hypothesis was that BSO treatment will affect blastocyst survival and gene expression associated with low embryo quality

overall_design: 4 replicates of 10 blast/rep was produced for BSO and control treatment. According to a dye swap design with 2 colors, 4 arrays were used to compare BSO (green) against CTL (red) and 4 arrays were used to compared BSO (red) againt CTL (green).


title: Transcriptional profiling of peripheral blood - comparison of results obtained from samples stored in two RNA stabilizing reagents

city: Turku

first: Tuomas

last: Nikula

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology

summary: RNA stabilizing reagents have been developed to ensure that transcription profiles of whole blood samples reflect the physiological state at the time of the blood drawn. Ability to preserve and maintain the in vivo gene expression status ex vivo is essential for gene expression profiling and biomarker discovery from clinical sample material.  We  compared transcriptional profiles obtained from samples collected using two established peripheral blood RNA collection systems, TEMPUS™ and PAXgene™. We demonstrated that TEMPUS™ and PAXgene™ systems can be used in combination with RiboAmp® mRNA amplification without a need for a separate globin reduction step. However, use of samples collected through different blood collection methods in the same experiment should be avoided.

overall_design: Two PAXgene and two TEMPUS blood RNA tubes were collected from three healthy volunteers (2 female and 1 male), in addition, pooled total RNA from PBMC of 41 normal blood donors was analyzed.

first: Juha

last: Mykkänen

first: Olli

last: Simell

first: Riitta

last: Lahesmaa


title: Montastraea franksi Control vs.  50 ppb Copper

status: Public on Oct 31 2012

city: Poughkeepsie

first: Jodi

last: Schwarz

address: 124 Raymond Ave

institute: Vassar College

summary: Gene expression profiling of corals exposed to control (ambient seawater) or 50 ppb copper for 24 hours

overall_design: Two-condition experiment, Control vs 50ppb. Biological replicates: 5 genotypes paired in control vs 50ppb, each genotype collected from different location on reef. One replicate per array.


title: The NIH Human Pluripotent Stem Cell Database (Agilent, miRNA)

city: Bethesda

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: MicroRNA profiling was performed on RNA samples matched to those included in the NIH Human Pluripotent Stem Cell Database (Series GSE32923). Twenty undifferentiated human embryonic stem cell lines and 4 human tissues were analyzed. Expanded descriptions of methods used are available at: http://stemcelldb.nih.gov.

overall_design: 49 samples: 38 human ESC (UNDIFFerentiated), 1 human Brain, 1 human Heart, 1 human Liver, 1 human Ovary and 7 processing controls (UniRef).

first: Barbara

last: Mallon

first: Josh

last: Chenoweth

first: Rebecca

last: Hamilton

first: Paul

last: Tesar

first: Amarendra

last: Yavatkar

first: Leonard

last: Tyson

first: Yang

middle: C

last: Fann

first: Kye

middle: Y

last: Park

first: Kevin

last: Chen

first: Ronald

last: McKay


title: AAPH-treated blastocysts vs CTL-treated blastocysts

first: Gael

last: Cagnone

summary: In order to understand how in vitro culture affects embryonic quality, we analyzed survival and global gene expression in bovine blastocysts after exposure to increased oxidative stress conditions of IVC. A pro-oxidant agents that act extra-cellularly by promoting ROS production (0.01 mM 2,2'-azobis (2-amidinopropane) dihydrochloride [AAPH]) was added from days 3 to 7, and transcriptomic analysis was then performed in resulting blastocysts. Precisely, after in vitro maturation and fertilization, bovine zygotes were culture in vitro in normal condition, then at day 3, embryos were allocated into culture in control or supplemented with AAPH (0.01 mM) until day 7. At this time, blastocysts were harvested and analyzed. Our hypothesis was that AAPH treatment will affect blastocyst survival and gene expression associated with low embryo quality

overall_design: 4 replicates of 10 blast/rep was produced for AAPH and control treatment. According to a dye swap design with 2 colors, 4 arrays were used to compare AAPH (green) against CTL (red) and 4 arrays were used to compared AAPH (red) againt CTL (green).


title: Colorectal Cancer Cell Lines aCGH

status: Public on Nov 02 2012

first: Keyan

last: Salari

state: MA

address: Gray/Bigelow Rm 1102, 55 Fruit Street

institute: Massachusetts General Hospital

summary: Somatic DNA alteration underlies tumor development and progression, and gives rise to tumors with diverse genetic contexts. Here, we identify in a collection of 29 colorectal cancer cell lines and 226 primary colorectal tumors recurrent amplification of chromosome 13, an alteration highly restricted to colorectal-derived cancers. A minimal region of amplification on 13q12.2 pinpoints caudal type homeobox transcription factor CDX2, a master regulator of anterior-posterior patterning, midgut development, and intestinal epithelial cell differentiation and maintenance. In contrast to its described role as a colorectal tumor suppressor, we show that in the context of genomic amplification, CDX2 is required for proliferation and anchorage-independent growth of colorectal cancer cells. By genome-wide expression and location analysis, we reveal that CDX2 directly promotes expression of Wnt pathway genes. Further results suggest that CDX2 induces expression of intestinal differentiation markers and modulates b-catenin transcriptional activity. These data characterize CDX2 as a novel lineage-survival oncogene deregulated in colorectal cancer.

overall_design: comparative genomic hybridization by array

first: Jonathan

last: Pollack


title: Cell-density resolved comparative analysis of D. shibae wild-type vs. delta-luxI1

status: Public on Nov 03 2012

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: A quorum sensing null mutant was compared with D. shibae wild-type in order to identify quorum sensing controlled traits in this organism. Samples were taken at different optical densities in the exponential phase and in the stationary phase in order to clarify if quorum sensing regulation is dependent on cell-densitiy

sample_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Samples from Dinoroseobacter shibae DFL 12 wild-type and delta-luxI1 (Dshi_0312) are compared during exponential (OD600 0.1, 0.2, 0.4, 0.6, 0.8) and stationary phase (6h post maximum OD600), two biological replicates

first: Diana

last: Patzelt

first: Hui

last: Wang

first: Ina

last: Buchholz

first: Alexander

last: Neumann

first: Johannes

last: Klein

first: Manfred

last: Rohde

first: Lothar

last: Gröbe

first: Silke

last: Pradella

first: Richard

last: Münch

first: Irene

last: Wagner-Döbler


title: Cell-density resolved comparative analysis of D. shibae wild-type vs. delta-luxI1 overexpressing luxI1 in trans

summary: D. shibae delta-luxI1 overexpressing the luxI1 gene in trans was compared to the wild-type in order to identify quorum sensing controlled traits in this organism. Samples were taken at different optical densities in the exponential phase and in the stationary phase.

platform_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Samples from Dinoroseobacter shibae DFL 12 wild-type and delta-luxI1pDP1 are compared during exponential (OD600 0.1, 0.2, 0.4, 0.6, 0.8) and stationary phase (6h post maximum OD600), two biological replicates


title: Comparative analysis of D. shibae wild-type vs. delta-luxI1 supplemented with different acetylated homoserine-lactones

summary: Comparison of a quorum sensing null mutant supplemented with C18-HSL, C18en-HSL, C18dien-HSL with D. shibae wild-type in order to identify traits induced by distinct autoinducers in this organism.

overall_design: Loop-design, two to three biological replicates of D. shibae wild-type, delta-luxI1 and delta-luxI1 supplemented with 500 nM C18-HSL, C18en-HSL and C18dien-HSL at cultivation start. Samples were taken in mid-exponential growth phase at OD600 0.4


title: Ten percent of aberrant cells is sufficient for detection of DNA copy number alterations (part 2)

status: Public on Oct 21 2012

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary: Array Comparative Genomic Hybridization (aCGH) is a widely used technique to assess chromosomal copy number alterations. Chromosomal content, however, is often not uniform throughout cell populations.  The aim of our present study is to evaluate to what extent aCGH can detect DNA copy number alterations in a heterogeneous cell population. Reported detection limits are a compound of analytical software and laboratory technique whilst systematic evaluation is lacking, despite the importance in diagnostics and research. Detection limits were explored with DNA isolated from a patient with intellectual disability (ID) and from tumor cell line BT474. Both were diluted with increasing amounts of normal DNA to simulate different levels of cellularity. Samples were hybridized on CGH arrays containing 180880 oligonucleotides evenly distributed over the genome (space ~17kb). The ID sample has a single copy number gain of 4Mb and a single copy number loss of 7.5Mb that could both be detected with 10% mosaicism. The tumor cell line BT474 has a dual copy number gain (6 copies in a background of 4 copies) of 46Mb. This corresponds to a single copy number gain in a diploid sample and could be detected with 15% tumor cells. The diagnostic validity of these findings was verified using two clinical mosaic samples with alterations in 20% (40Mb) and 14% (34Mb) of cells. Both alterations could be accurately detected using t-statistics.  In conclusion, single copy number gains and losses, down to 4Mb in as little as 10% of a cell population, can be detected by aCGH.

overall_design: Dilution range of breast cancer cell line BT474.

first: Oscar

last: Krijgsman

first: Danielle

last: Israeli

first: Hendrik

middle: F

last: van Essen

first: Paul

middle: P

last: Eijk

first: Michel

last: Berens

first: Clemens

last: Mellink

first: Aggie

middle: W

last: Nieuwint

first: Marjan

last: Weiss

first: Renkse

last: Steenbergen

first: Gerrit

last: Meijer

first: Bauke

last: Ylstra


title: qRT-PCR analysis of primary CD36+ cells infected with parvovirus B19

status: Public on Nov 04 2012

city: Gainesville

first: Igor

last: Ignatovich

state: FL

department: Psychiatry

institute: University of Florida

summary: The goal of our present work was to understand the influence parvovirus B19 infection may have on the thyroid hormone signaling pathway, as well as the nuclear receptors (NR) pathway overall. We demonstrated that B19 infection of CD36+ erythroid progenitor cells leads to downregulation of the thyroid hormone receptor α isoform. In addition to that we have shown that B19 infection modulates the expression of other members of the NR superfamily such as estrogen and retinoid receptors.

overall_design: CD36+ cells (StemCell Technologies) were mock-infected or infected with B19, 48 hours post infection cells were collected, total RNA was isolated, and cDNA was obtained as described above. TaqMan® array human nuclear receptors fast 96-well plates obtained from Applied Biosystems (Carlsbad, CA) were utilized in order to assess the differences of 92 nuclear receptors’ expression in mock- and B19-infected CD36+ cells.  Relative quantity (RQ) values were calculated using the 2-ΔΔCt method.


title: Genetic differences in transcript responses to low-dose ionizing radiation identify tissue functions associated with breast cancer susceptibility.

status: Public on Nov 01 2012

city: Berkeley

first: Antoine

middle: M

last: Snijders

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

summary: This study investigates three radiation exposure scenarios in BALB/c and C57BL/6 mice: (1) low dose (LD) group -- four weekly doses of 7.5 cGy, (2) high dose (HD) group -- four weekly doses of 1.8 Gy, (3) unexposed group -- four weekly sham exposures. We then used comparative expression profiles of the mouse mammary gland and cardiac blood to build a model of candidate tissue functions associated with LD cancer susceptibility in these strains and murine and human knowledgebases to characterize these tissue functions and their relevance to breast cancer.

overall_design: All samples were assessed on Affymetrix MOE 430 A arrays (HT_MG-430A; GPL8759).  Mammary gland tissues: 43 samples (2 strains, 3 treatments, 2 timepoints, 2-4 replicates).  For Cardiac blood tissue: 8 samples (2 strains, 4 replicates)

first: Andrew

middle: J

last: Wyrobek

first: Francesco

last: Marchetti

first: Sandhya

last: Bhatnagar

first: Nadire

last: Duru

first: Ju

last: Han

first: Zhi

last: Hu

first: Jian-Hua

last: Mao

first: Joe

last: Gray


title: Effect of dietary supplementation with direct fed microbials (DFM) in chicken

city: Beltsville

first: Duk Kyung

last: Kim

state: MD

address: Bldg. 1043, BARC-East

institute: USDA, ARS

summary: This study utilized comparative global gene expression microarray analysis to evaluate the effects of DFM on intestinal immunity of chicken.

overall_design: Two-condition experiment, DFM-fed chickens vs. Non-treated control chickens. Biological replicates: 2 control replicates, 2 DFM-fed replicates with dye-switching.

first: Duk

middle: K

first: Hyun

middle: S

last: Lillehoj


title: Mammary carcinomas in WAP-SV40 transgenic mice [aCGH]

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

summary: Transgenic expression in mice of two synergistically acting SV40 early region encoded proteins, large (LT) and small (sT) tumor antigens, in the mammary epithelium recapitulates loss of p53 and Rb function and deregulation of PP2A-controlled mitogenic pathways in human breast cancer. In primiparous mice, WAP-promoter driven expression of SV40 proteins induces well and poorly differentiated mammary adenocarcinomas. We performed a correlative aCGH and gene expression analysis of 25 monofocal tumors, representing four histopathological grades, to explore the molecular traits of SV40-induced mammary tumors and to emphasize the relevance of this tumor model for human breast tumorigenesis.

overall_design: CGH analysis of 15 mammary carcinoma samples of the NP8 WAP-SV40 mouse line.

first: Genrich

last: Tolstonog

first: Benjamin

last: Otto

first: Wolfgang

last: Deppert


title: Involuted normal mammary gland in WAP-SV40 transgenic mice [gene expression]

overall_design: Gene expression analysis of 6 involuted normal mammary gland 30 days post weaning in WAP-SV40 T1 and BALB/c samples.


title: Oncogenic mutation in Smoothened causes severe cerebellar developmental defects and medulloblastoma in mice

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck and Co., Inc.

summary: Deregulated developmental processes in the cerebellum cause medulloblastoma, the most common malignant tumor of the central nervous system. About 20-30% of cases are caused by mutations increasing the activity of the Sonic hedgehog (Shh) pathway, a critical mitogen in cerebellar development. The proto-oncogene Smoothened is a key transducer of the Shh pathway. Activating mutations in Smoothened that lead to constitutive activity of the Shh pathway have been identified in human medulloblastoma. To understand the molecular and cellular effects of Smoothened variants in normal development and medulloblastoma genesis, we generated the SmoA2 transgenic mouse model which expresses the transgene exclusively in granule neuron precursors. In this study, we demonstrate how two point mutations in a single molecule can produce starkly different phenotypes as seen in comparison to our previous model, ND2:SmoA1. The SmoA2 mice have severe aberrations in cerebellar development whereas the SmoA1 mice are largely normal during development. Medulloblastomas in the SmoA2 mice develop in the dysplastic cerebellar milieu. Intriguingly, despite disruptions in the stereotypic organization of the cerebellum, the SmoA2 mice do not exhibit any overt abnormalities in motor coordination. The differences in the global transcriptional profiles downstream of SmoA1 and SmoA2 further demonstrate the distinctiveness of the two oncogenic Smoothened mutations. The SmoA2 model serves as a unique spatiotemporal tool to investigate the functional significance of the reiterative cerebellar circuitry as well as to further understand Shh pathway mechanics in cerebellar development and oncogenesis.

overall_design: We previously generated a SmoA1 transgenic mouse medulloblastoma model, which expresses the SmoA1 transgene driven by the GNP-specific fragment of the promoter of ND2 transcription factor leading to constitutively active Shh signaling exclusively in the cerebellum.  In this study, we characterize the ND2:SmoA2 transgenic mouse model with a similarly designed transgene expressing the SmoA2 mutation. To assess transcriptional changes downstream of SmoA1 and SmoA2, we evaluated global gene expression profiles of P5 SmoA1, SmoA2 and Wt age-matched cerebella. We chose this specific developmental stage because (1) the phenotypes of SmoA1 and SmoA2 are robust and distinct at P5; (2) at P5 GNPs undergo proliferation, migration and differentiation and therefore expression profiling could capture key differences in multiple processes.

first: Joyoti

last: Dey

first: James

last: Olson

first: Janell

last: Schelter


title: Ten percent of aberrant cells is sufficient for detection of DNA copy number alterations (part 5)

first: Daoud

last: Sie

overall_design: DNA of a chronic lymphocytic leukemia (CLL) patient with mosaic aberrations in chromosome 12.

first: Oscar

last: Krijgsman

first: Danielle

last: Israeli

first: Hendrik

last: van Essen

first: Paul

last: Eijk

first: Michel

middle: L

last: Berens

first: Clemens

last: Mellink

first: Aggie

last: Nieuwint

first: Marjan

last: Weiss

first: Renkse

middle: D

last: Steenbergen

first: Gerrit

middle: A

last: Meijer

first: Bauke

last: Ylstra


title: Transcriptional analysis of wild-type and delta_dasR mutant of Streptomyces coelicolor grown in soil amended with chitin

city: Tsukuba

first: Behnam

last: Nazari

state: Ibaraki

address: 3-1-3 Kannondai

department: Environmental Biofunction Division

institute: National Institute for Agro-Environmental Sciences

summary:
Genome-wide microarray analysis was performed using RNA extracted from soil cultures of Streptomyces coelicolor A3(2) in the presence or absence of chitin. The vast majority of genes in chitin and amino sugar metabolism, as well as many other genes for carbon and energy, nitrogen and sulfur metabolism, were differentially expressed in response to addition of chitin. Moreover, the gene expressions of eight gene clusters for secondary metabolites were also significantly up-regulated in the chitin amended soil.
To reveal the role of a pleiotropic transcriptional regulator, DasR, which has been reported to be involved in regulation of chitin metabolism, antibiotic production and morphological differentiation, the gene expression patterns of wild type and dasR mutant in soil amended with chitin were compared by microarray analysis. The dasR mutation resulted in up-regulation of four antibiotic gene clusters and down-regulation of chitin metabolism.

overall_design: A study using total RNA extracted from soil cultures of Streptomyces ceolicolor A3(2). A whole genome microarray of S. coelicolor (NimbleGen Custom Prokaryotic Gene Expression 72K 4-plex Arrays) was designed and manufactured by Roche (Roche NimbleGen, Madison, WI). Each array contained four sets of 8 sequence-specific 60-mer probes per gene corresponding to 7825 genes from the S. coelicolor A3(2) genome.

first: Michihiko

last: Kobayashi

first: Akihiro

last: Saito

first: Azam

last: Hassaninasab

first: Kiyotaka

last: Miyashita

first: Takeshi

last: Fujii


title: array-CGH on single blastomeres from day-3 human cleavage stage embryos

status: Public on Oct 15 2012

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

summary: Seventy blastomeres from fourteen frozen-thawed supernumerary human preimplantation embryos were disassociated and genomic was amplified using Multiple Displacement Amplification. BAC array-CGH was performed on the amplified products.

overall_design: BAC array-CGH on single blastomeres amplified by Multiple Displacement Amplification.

first: Afroditi

last: Mertzanidou

first: Leeanda

last: Wilton

first: Jiqiu

last: Cheng

first: Evelyne

last: Vanneste

first: Yves

last: Moreau

first: Joris

last: Vermeesch

first: Karen

last: Sermon


title: Analysis of gene expression in MyD88-Knockdown-Hydra vulgaris (AEP)

status: Public on Oct 08 2012

city: Kiel

first: Sören

last: Franzenburg

address: Am Botanischen Garten 1-9

department: cell- and developmental biology

institute: zoological institute Kiel

summary: Analysis of MyD88 as a putative mediator in host-microbe-interactions

overall_design: MyD88-Hairpin was micro-injected in Hydra AEP embryos. The resulting Hatchling D3 showed a patchy distribution of the transgene observed by GFP. By asexual reproduction via budding and constant selection for the marker gene GFP the transgene could be driven into different cell ines. Therefore two different cultures were established. Polyps that showed no GFP-Signal anymore (control) and Polyps with both, endodermal and ectodermal transgenic cell-lines (knockdown).

first: S

last: Fraune

first: T

last: Bosch

last: Domazet-Loso


title: Gene expression profiling of PC3 cells stably expressing ERbeta1 and ERbeta2

status: Public on Oct 03 2012

city: Houston

first: Philip

last: Jonsson

state: TX

address: Department of Biology and Biochemistry – NSM Center for Nuclear Receptors and Cell Signaling 3605 Cullen Blvd, Science & Engineering Research Center Bldg 545

country: USA

institute: University of Houston

summary: The estrogen receptor (ER)β1 is successively lost during cancer progression, whereas its splice variant, ERβ2, is expressed in advanced prostate cancer. The latter form of cancer often metastasizes to bone, and we wanted to investigate whether the loss of ERβ1 and/or the expression of ERβ2 affect such signaling pathways in prostate cancer. Using PC3 and 22Rv1 prostate cancer cell lines that stably express ERβ1 or ERβ2, we found that the ERβ variants differentially regulate genes known to affect tumor behavior. We found that ERβ1 repressed the expression of the bone metastasis regulator Runx2 in PC3 cells. By contrast, RUNX2 expression was up-regulated at the mRNA level by ERβ2 in PC3 cells, whereas Slug was up-regulated by ERβ2 in both PC3 and 22Rv1 cells. In addition, the expression of Twist1, a factor whose expression strongly correlates with high Gleason grade prostate carcinoma, was increased by ERβ2. In agreement with the increased Twist1 expression, we found increased expression of Dickkopf homolog 1; Dickkopf homolog 1 is a factor that has been shown to increase the RANK ligand/osteoprotegerin ratio and enhance osteoclastogenesis, indicating that the expression of ERβ2 can cause osteolytic cancer. Furthermore, we found that only ERβ1 inhibited proliferation, whereas ERβ2 increased proliferation. The expression of the proliferation markers Cyclin E, c-Myc, and p45(Skp2) was differentially affected by ERβ1 and ERβ2 expression. In addition, nuclear β-catenin protein and its mRNA levels were reduced by ERβ1 expression. In conclusion, we found that ERβ1 inhibited proliferation and factors known to be involved in bone metastasis, whereas ERβ2 increased proliferation and up-regulated factors involved in bone metastasis. Thus, in prostate cancer cells, ERβ2 has oncogenic abilities that are in strong contrast to the tumor-suppressing effects of ERβ1.

overall_design: The GFP vs. ERbeta1 comparison was carried out with three replicate dye-swaps, six arrays total. The GFP vs. ERbeta2 comparison was carried out with two replicate dye-swaps, four arrays total.

first: Prasenjit

last: Dey

first: Johan

last: Hartman

first: Cecilia

last: Williams

first: Anders

last: Ström

first: Jan-Åke

last: Gustafsson


title: Methylome analysis of epiRIL344 BC1-S1 to BC1-S6  aerial part

status: Public on Sep 03 2012

city: PARIS

first: Vincent

last: Colot

address: 46 rue d'Ulm

institute: IBENS - CNRS UMR8197 - INSERM U1024

type: Methylation profiling by genome tiling array

summary:
DNA methylation profiling in epiRIL344 BC1-S1 to BC1-S6  aerial part (epiRIL344_BC1-S1 - epiRIL344_BC1-S2 - epiRIL344_BC1-S3 - epiRIL344_BC1-S4 - epiRIL344_BC1-S5 - epiRIL344_BC1-S6)

Keywords: Genome binding/occupancy profiling by genome tiling array

overall_design: 1 biological replicate in dye-swap - MeDIP-chip

first: Mathilde

last: Etcheverry

first: Maria

last: Colomé-Tatché

first: René

last: Wardenaar

last: Duvernois-Berthet

first: Frank

last: Johannes


title: miRNA profiling data of mouse bone marrow samples four days post 5-FU treatment versus untreated controls

status: Public on Sep 24 2012

city: New Haven

first: Brian

last: Adams

state: CT

address: 10 Amistad Street; Rm214K

department: Genetics

institute: Yale University

summary: To identify miRNAs that regulate hematopoietic response after 5-FU-induced injury, we analyzed miRNA expression changes in bone marrow cells from mice with or without 5-FU treatment. Global miRNA expression profiling of the 5-FU and untreated cohorts showed that 92 miRNAs (among 168 that passed the detection threshold) were significantly upregulated or downregulated, with false discovery rates < 5%.

overall_design: Female 6wk-old C57Bl6/J mice were left untreated or given a single dose of 5-FU (150mg/kg).  Four days post treatment whole bone marrow was isolated from each animal (n=3 for treated and n=5 for untreated controls) and lysed for total RNA using Trizol (Invitrogen).  Samples were profiled for miRNA expression using a bead-based profiling methodology (Lu et al., 2008). Profiling data were normalized assuming equal total miRNA expression across samples. Differential miRNA expression was analyzed by student’s t-test and then calculated for false discovery rate using the Benjamini and Hochberg method.

first: Shangqin

last: Guo

first: Haito

last: Bai

first: Yanwen

first: Cynthia

last: Megyola

first: Jijun

last: Cheng

first: Kartoosh

last: Heydari

first: Changchun

last: Xiao

first: E

last: Reddy

first: Jun

last: Lu


title: Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80

status: Public on Sep 29 2012

city: No.12 Zhongguancun South Street, Haidian

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

summary: Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions play important roles in key biological processes.Analysis of published transcriptom datasets suggested some lincRNAs may be regulated by SERRATE,CBP20 and CBP80 in Arabidopsis. To further investigate the regulation, we use Arabidopsis lincRNA arrays v1 to detect lincRNA expression in se-2 and cbp20/80 double mutants.We found the expression levels of 940 lincRNAs (20%) out of the 4,634 lincRNAs with probes in array were significantly alerted in all mutants (P-value of eBays ANOVA < 0.05 & fold change of signal intensity > 2). This group included 525 up-regulated and 415 down-regulated lincRNAs.

overall_design: Seedlings(Col-0), Seedlings(se-2), Seedlings(cbp20,80 double mutant) x 3 biological replicates

last: Xu

first: Choonkyun

last: Jung

first: Lucia

last: Bernad

first: Huan

last: Wang

first: Catalina

last: Arenas

first: Jing-jing

last: Jin

first: Limsoon

last: Wong

first: Nam-Hai

last: Chua


title: Methylome analysis of 123 epiRILs, WT and ddm1 mutant aerial part

first: Vincent

last: Colot

summary:
DNA methylation profiling in 123 epiRILs, WT and ddm1 mutant aerial part (epiRIL008 - epiRIL011 - epiRIL014 - epiRIL018 - epiRIL020 - epiRIL024 - epiRIL036 - epiRIL046 - epiRIL052 - epiRIL053 - epiRIL054 - epiRIL055 - epiRIL060 - epiRIL062 - epiRIL064 - epiRIL069 - epiRIL070 - epiRIL071 - epiRIL073 - epiRIL092 - epiRIL093 - epiRILv94 - epiRIL095 - epiRIL098 - epiRIL099 - epiRIL101 - epiRIL108 - epiRIL112 - epiRIL114 - epiRIL118 - epiRIL122 - epiRIL137 - epiRIL144 - epiRIL147 - epiRIL148 - epiRIL150 - epiRIL159 - epiRIL164 - epiRIL166 - epiRIL169 - epiRIL170 - epiRIL172 - epiRIL183 - epiRIL193 - epiRIL195 -  - epiRIL202 - epiRIL208 - epiRIL215 - epiRIL216 - epiRIL218 - epiRIL222 - epiRIL225 - epiRIL229 - epiRIL232 - epiRIL238 - epiRIL244 - epiRIL252 - epiRIL257 - epiRIL258 - epiRIL260 - epiRIL262 - epiRIL275 - epiRIL276 - epiRIL277 - epiRIL297 - epiRIL305 - epiRIL315 - epiRIL323 - epiRIL326 - epiRIL333 - epiRIL340 - epiRIL344 - epiRIL350 - epiRIL356 - epiRIL362 - epiRIL361 - epiRIL363 - epiRIL366 - epiRIL368 - epiRIL371 - epiRIL375 - epiRIL391 - epiRIL393 - epiRIL394 - epiRIL400 - epiRIL408 - epiRIL410 - epiRIL425 - epiRIL432 - epiRIL434 - epiRIL437 - epiRIL438 - epiRIL439 - epiRIL454 - epiRIL458 - epiRIL466 - epiRIL467 - epiRIL471 - epiRIL473 - epiRIL477 - epiRIL480 - epiRIL488 - epiRIL492 - epiRIL493 - epiRIL494 - epiRIL495 - epiRIL497 - epiRIL500 - epiRIL503 - epiRIL506 - epiRIL508 - epiRIL523 - epiRIL538 - epiRIL539 - epiRIL556 - epiRIL558 - epiRIL559 - epiRIL561 - epiRIL567 - epiRIL570 - epiRIL572 - epiRIL573 - epiRIL579 - wt - ddm1 mutant)

Keywords: Genome binding/occupancy profiling by genome tiling array

first: Sandra

last: Cortijo

first: Maria

last: Colomé-Tatché

first: René

last: Wardenaar

first: Evelyne

last: Duvernois-Berthet

first: Frank

last: Johannes


title: Transcriptome analysis of ddm1 Arabidopsis mutant, epiRIL98 and epiRIL202

type: Expression profiling by genome tiling array

first: Antoine

last: Martin


title: Using microarrays to investigate differential gene expression in gills from smallmouth bass after various exposures.

status: Public on Aug 31 2012

city: Alachua

first: Barbara

middle: Joan

last: Carter

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

summary: The purpose of this study was to investigate differentially expressed genes in gill and liver tissue from smallmouth bass (Micropterus dolomieu) after exposure to various treatments, compared to controls.  The treatments consisted of bacteria, estradiol, and a mixture of bacteria plus estradiol.

sample_organism:
Micropterus salmoides
Micropterus dolomieu

overall_design: Four-condition experiment with biological replicates: 4 control replicates, 4 of each treatment for liver and gill tissue.

first: Laura

last: Robertson


title: Methylation in breast cancer vs. normal tissue

status: Public on Sep 14 2012

city: Heidelberg

first: Marta

last: Faryna

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: We applied a combination of Methyl-CpG Immunoprecipitation (MCIp) and Human CpG Island microarrays to identify aberrant DNA methylation in eight low-grade breast invasive carcinomas and two pre-invasive breast tumors against ten normal breast tissues.

overall_design: 10 breast tumor samples (8 invasive, 2 pre-invasive) and 10 normal breast tissues, paired randomly (except Array 10: matched pair)

first: Carolin

last: Konermann


title: Expression data from  E2f7/E2f8 and E2f1/E2f2/E2f3 null and wild type liver along with E2f7/E2f8 null and wild type trophoblast giant cells (nCounter)

city: Columbus

first: Madhu

last: Ouseph

state: Ohio

address: 460w 12th Ave

institute: The Ohio State University

summary: To understand the underlying cause and mechanisms of changes in hepatocyte ploidy upon Albumin-Cre mediated deletion of E2f7&8 and Mx1-Cre mediated deletion of E2f1,2&3 and germline deleted trophoblast giant cells, we analysed global gene expression of 6 weeks and 2 months liver tissues.

overall_design: RNA was extracted from liver tissues using trizol method and Arcturus PicoPure RNA Isolation Kit for laser capture microdisected trophoblast giant cells. Gene deletion in samples confirmed by PCR genotyping of DNA isolated from each sample.

first: M

first: H

last: Chen

first: T

last: Pecot


title: Methylated CpG island amplification (MCA) microarray analysis of human gastric mucosa and cancer

status: Public on Sep 01 2012

city: Sapporo

first: Eiichiro

last: Yamamoto

address: South-1, West-16, Chuo-ku

institute: Sapporo medical university

summary:
Aberrant DNA methylation is implicated in the epigenetic field defect seen in gastric cancer (GC).
Our aim in this study was to identify predictive biomarkers by screening for DNA methylation in noncancerous background gastric mucosa from GC patients.

overall_design:
A total of 46 endoscopically obtained human gastric mucosa, 10 gastric cancer and 5 cell lines were analyzed using MCA microarray. Aberrant DNA methylation was compared with clinicopathological features.

Healthy individuals were divided into two groups based on the types of chronic gastritis;
A: antrum-predominant gastritis
P or C: pangastritis or corpus-predominant gastritis

first: Hiromu

last: Suzuki


title: Modulators of Prostate Cancer Cell Proliferation and Viability Identified by Short-Hairpin RNA Library Screening

city: Chapel Hill

first: Joel

last: Parker

state: NC

address: 5109 B Bioinformatics Building

institute: UNC - CH

summary: Recovery of hairpins targeting a known prostate cancer pathway testing the utility of shRNA library screening in prostate cancer as a broad strategy to identify new candidate drug targets.

overall_design: Two cell lines assayed  for 4 time points with a control and 2 experimental conditions.  Two to four replicates of each instance are provided.

first: Kimberly

middle: B

last: Dahlman


title: Global changes in gene expression of grapefruit peel tissue in response to the yeast biocontrol agent M. fructicola

status: Public on Aug 21 2012

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary:
This work explores the biochemical responses of surface wonds of fruit to yeast pathogens.
Results indicate that significant expression changes occur following wounding and yeast application compared to wounded controls. These changes included a range of defense-related oxidative, signalling and secondary metabolism genes.

overall_design: Three reps each of control (grapefruit peel) and grapefruit peel following Metschnikowia fructicola treatment.

first: V

last: Hershkovitz

first: C

last: Ben-Dayan

first: L

last: Cohen

first: G

last: Raphael

first: J

last: Liu

first: E

last: Belausov

last: Wisniewski

first: S

last: Droby


title: Molecular analysis of growth-limiting drought stress in Brachypodium leaves

status: Public on Oct 01 2012

city: Ghent

first: Stefanie

last: De Bodt

address: Technologiepark 927

institute: VIB/UGent

summary: To explore the usefulness of Brachypodium distachyon for drought studies, a reproducible in soil drought assay was developed. Spontaneous soil drying led to a 45% reduction in leaf size, and this most mostly due to a decrease in cell expansion, whereas cell division remained largely unaffected by drought. To investigate the molecular basis of the observed leaf growth reduction, Brachypodium leaf 3 was dissected in three zones, namely the proliferation, expansion and mature zone, and subjected to transcriptome analysis using a Affymetrix whole-genome tiling array. This approach allowed us to highlight that transcriptome profiles of different developmental leaf zones respond differently to drought. Several genes and biological processes involved in drought tolerance were identified. Mainly, we observed an increased energy availability in the proliferation zone along with an upregulation of sterol synthesis that may influence membrane fluidity.

overall_design: 24 samples of Brachypodium leaf 3 harvested about 24 hours after the emergence of leaf 3, mild drought stress was performed for 2 biological replicates, severe drought stress and control condition was performed for 3 biological replicates. 3 developmental zones, namely the proliferation, expansion and mature zone, are dissected from leaf 3.

first: Dirk

last: Inzé

first: Wim

last: Verelst


title: Identification of differently expressed genes in Rainbow trout muscle under restricted feeding

status: Public on Aug 18 2012

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

summary: We identified that the adiponectin gene expression in rainbow trout muscle decreased by restrected feeding. In order to identify the genes differently expressed by the same treatment, micrarray analysis was conducted

overall_design: Fish were fed ad libitum once a week (RF, restricted feed group) or fed ad libitum twice per day (control).  After 1 month, the muscle was desected from 4 individuals from each group.

first: Satomitsu

last: Suda

first: Yuriko

last: Kawana

first: Ikuo

last: Hirono

first: Reiko

last: Nagasaka

first: Gen

last: Kaneko

first: Hideki

last: Ushio

first: Shugo

last: Watabe


title: Array CGH comparison of genomic sequence content between tissues from the same animal

status: Public on Aug 19 2012

city: Lexington

first: Jeramiah

last: Smith

state: KY

address: 101 T.H. Morgan Building

institute: University of Kentucky

summary:
DNA was isolated from tissues (blood, sperm, or liver). DNA from different tissues from the same organism were labeled with alternate fluorophores (Cy3 or Cy5)
and hybridized to a custom array that was designed from lamprey (Petromyzon marinus) genomic sequence.

overall_design: 1 animal - sperm vs. blood, 2 animals - blood vs. liver

first: Carl

last: Baker

first: Evan

middle: E

last: Eichler

first: Chris

middle: T

last: Amemiya


title: An integrated genomic and expression analysis of 7q deletion in SMZL (Oligo aCGH)

status: Public on Aug 30 2012

city: Cambridge

first: Alan

last: Watkins

address: Addenbrooke's Hospital

institute: University of Cambridge

summary:
Splenic marginal zone lymphoma (SMZL) is an indolent B-cell lymphoproliferative disorder characterised by 7q32 deletion, but the target genes of this deletion remain unknown.  In order to elucidate the genetic target of this deletion, we performed an integrative analysis of the genetic, epigenetic, transcriptomic and miRNomic data.  High resolution array comparative genomic hybridization of 56 cases of SMZL delineated a minimally deleted region (2.8Mb) at 7q32, but showed no evidence of any cryptic homozygous deletion or recurrent breakpoint in this region.  Integrative transcriptomic analysis confirmed significant under-expression of a number of genes in this region in cases of SMZL with deletion, several of which showed hypermethylation.   In addition, a cluster of 8 miRNA in this region showed under-expression in cases with the deletion, and three (miR-182/96/183) were also significantly under-expressed (P <0.05) in SMZL relative to other lymphomas.   Genomic sequencing of these miRNA and IRF5, a strong candidate gene, did not show any evidence of somatic mutation in SMZL.

Keywords: Genome variation profiling by genome tiling array

overall_design: For aCGH. 21 fresh frozen splenic samples from patients with SMZL were hybridized against a reference control of pooled PBMC genomic DNA from 10 normal subjects. High-resolution oligonucleotide analysis of copy number variations in splenic marginal zone lymphoma (SMZL) in regions of recurrent alteration. Regions included on the array: 7q (2k resolution) and regions of interest on chromosomes 3q, 6q and 9q at 12k resolution.

first: Rifat

last: Hamoudi

first: Naiyan

last: Zeng

first: Qingguo

last: Yan

first: Yuanxue

last: Huang

first: Hongxiang

last: Liu

first: Jianzhong

last: Zhang

first: Esteban

last: Braggio

first: Rafael

last: Fonseca

first: Laurence

last: de Leval

first: Peter

middle: G

last: Isaacson

first: Andrew

last: Wotherspoon

first: Ellen

last: McPhail

first: Ahmet

last: Dogan

first: Ming

middle: Q

last: Du


title: Pleiotropic roles of Msi1-like protein, Msl1, in growth, differentiation, stress response, and virulence of Cryptococcus neoformans

status: Public on Aug 23 2012

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

summary: WD40 motif-containing Msi1-like (MSIL) proteins play pleiotropic cellular functions as a negative regulator of the Ras/cAMP-pathways and a component of chromatin assembly factor-I (CAF-I), and yet have not been studied in fungal pathogens. Here we identified and characterized an MSIL protein, Msl1, in Cryptococcus neoformans, which can cause fatal meningoencephalitis in humans. Notably, Msl1 was not a functional ortholog for the yeast Msi1 but played pleiotropic roles in C. neoformans in both cAMP-dependent and -independent manners but mainly Ras-independently. Msl1 negatively controlled antioxidant melanin production and sexual differentiation, which can be repressed by inhibiting the cAMP-signaling pathways. In contrast, Msl1 controlled thermotolerance, diverse stress responses, and antifungal drugs resistance in Ras/cAMP-independent manners. Cac2, which is the second CAF-I component, appeared to play both redundant and distinct function with Msl1. Msl1 is required for full virulence of C. neoformans. Transcriptome and proteomic analysis identified a group of Msl1-regulated genes or -interacting proteins, respectively, which mostly include stress-related genes, including HSP12, HSP78, SSA1, SSA4, and STM1. Furthermore, we identified the third putative component of CAF-1, Rlf2, in C. neoformans. In conclusion, this study demonstrated the pleiotropic roles of Msl1 in human fungal pathogen C. neoformans, providing a novel antifungal therapeutic target.

sample_organism:
Cryptococcus neoformans
Cryptococcus neoformans H99

overall_design: There is more than 95% genome homology between JEC21 and H99. Therefore, 6 slides of JEC21 (Cryptococcus neoformans var. neoformans serotype D) 70-mer oligos are used in this analysis. Total RNAs are extracted from 2 strains from H99 (H99 wild-type strain (Cryptococcus neoformans var. grubii serotype A), msl1Δ). 3 biological replicate experiments are performed for each strain. We use the mix of all total RNAs from this experiment as the control RNA. We use Cy3 as the test sample dye and Cy5 as the control dye.

first: Dong

middle: H

last: Yang

first: Shinae

last: Maeng

first: Anna

last: Strain

last: Floyd

first: Kirsten

last: Nielsen

first: Joseph

last: Heitman

first: Yong


title: aCGH on somatic tissues from 6 human subjects

status: Public on Aug 16 2012

city: Palo Alto

first: Maeve

last: O'Huallachain

state: CA

address: 1501 S. California Ave. Rm 2204

institute: Stanford University

summary: Somatic tissues were hybridized against a reference tissue selected for each subject. Two hybridizations were performed for each tissue comparison (regular and dye-swap)

overall_design: Somatic human tissue aCGH tissue comparison

first: Michael

last: Snyder