title: Expression profile of porcine alveolar macrophages after in vitro stimulation with LPS from Salmonella typhimurium

city: CORDOBA

first: JUAN JOSE

middle: GARRIDO

last: PAVÓN

state: CORDOBA

address: Edificio Gregor Mendel (C5)

department: GENÉTICA

institute: UNIVERSITY OF CÓRDOBA

summary: The objective of this study was to identify porcine genes which expression was affected in vitro stimulation with LPS from Salmonella typhimurium. Microarray experiment was conducted to reveal genes being significantly differentially expressed in LPS stimulated versus unstimulated porcine alveolar macrophages from two from healthy pigs

overall_design: The comparison was done LPS alveolar macrophages versus unstimulated alveolar macrophages sampled from two healthy pigs. The experiment was conducted as common reference design.

first: Ángeles

last: Jiménez-Marín

first: Jakob

last: Hedegaard

first: Mónica

last: Pérez-Alegre

first: Juan

last: Garrido


title: Expression profiles of histone point mutants

status: Public on Dec 04 2013

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

summary: Accurate chromosome segregation requires that sister kinetochores biorient and attach to microtubules from opposite poles.  Kinetochore biorientation relies on the underlying centromeric chromatin, which provides a platform to assemble the kinetochore and to recruit the regulatory factors that ensure the high fidelity of this process. To identify the centromeric chromatin determinants that contribute to chromosome segregation, we performed two complementary unbiased genetic screens using a library of mutants in every residue of histone H3 and H4. In one screen, we identified mutants that lead to increased loss of a non-essential chromosome. In the second screen, we isolated mutants whose viability depends on a key regulator of biorientation, the Aurora B protein kinase. Nine mutations, H3 Q5A, H3 R40A, H3 G44A, H3 R53A, H3 N108A, H3 L109A, H4 K44A, H4 V81A, and H4 Y98A, were common to both screens and exhibited kinetochore biorientation defects.  Five of the mutants map near the unstructured nucleosome entry site and their genetic interaction with decreased Ipl1 function can be suppressed by increasing the dosage of the Sgo1 protein. In addition, the composition of purified kinetochores was altered in five of the mutants. Together, this work identifies previously unknown histone residues involved in chromosome segregation and lays the foundation for future studies of the role of the underlying chromatin structure in segregation.

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.

first: Tessie

last: Ng

first: Junbiao

last: Dai

first: Nicole

last: Duggan

first: Tineke

last: Lenstra

first: Frank

last: Hostege

first: Jef

last: Boeke

first: Sue

last: Biggins


title: Glucocorticoid effect on mRNA translation in childhood acute lymphoblastic leukemia

status: Public on Dec 03 2013

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
Glucocorticoids (GCs) are a central component in treating childhood acute lymphoblastic leukemia (chALL). They mainly act via regulating gene transcription. However, control of mRNA translation by GC has never been assessed systematically. In our research, T- and precursor B-ALL cells were cultured with and without GC for 6 hours and subjected to translational profiling, a technique combining sucrose gradient fractionation and microarray analysis of mRNA in different fractions. Analysis of GC regulation in different pools revealed no significant differences in regulation of mRNA translation by GC, suggesting no evidence for translational regulation by GC.
Ribosome profiling by sucrose gradient fractionation followed by microarray analysis of RNA from 3 distinct pools representing free RNA (pool 1), RNA in small protein-RNA complexes or bound to single ribosomes (pool 2) and RNA from large protein-RNA complexes (polysomes, pool 3). See Material and Methods of the original article for a detailed description.

overall_design: Translational efficiency of genes was estimated by comparing the amount of a gene's mRNA in pool 3 with the total amount of mRNA of the gene (in all 3 pools). Translational regulation by GC was estimated by contrasting gene regulations in pool 3 with gene regulation between GC-treated and control samples in all 3 pools (depicted as transcriptional regulation). Moderated t-tests were used to assess significance for translational regulation.

first: Tatsiana

last: Aneichyk

first: Daniel

last: Bindreither

first: Reinhard

last: Kofler


title: Dynamics of intercellular and extracellular (exosomal) miRNAs in hypoxic SUDHL4 cells

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

summary: Recently, the existence of extracellular miRNAs enclosed in exosomes has raised the possibility that they play an important role in cell-cell communication. To gain more insight into cell-cell communication via exosomal miRNAs, we investigated whether or not tumor cells exposed to hypoxia secrete exosomes which may affect angiogeneic activity. We used SUDHL4 cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from SUDHL4 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h were used for validation of angiogeneic activity, such as tube formation assay. The exosome secreted from SUDHL4 cells in hypoxic condition significantly enhanced tube formation by HUVECs when compared with exosome obtained from SUDHL4 cell in normoxic condition. To identify cellular and exosomal miRNAs universally responding to hypoxic condition, we assess the expression profiles of intercellular and extracellular miRNAs in SUDHL4 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA).

overall_design: SUDHL4 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).


title: Transcriptomic analysis of chlorhexidine shock in Acinetobacter baumannii

city: North Ryde

first: Karl

middle: Adam

last: Hassan

state: NSW

address: Eastern Rd, Macquarie University

department: Dept. Chemistry and Biomolecular Sciences

country: Australia

institute: Macquarie University

summary: In this study the transcriptomic changes occurring in A. baumannii ATCC 17978 in response to shock treament using the biocide chlorhexdine were determined. A. baumannii ATCC 17978 cells were grown at 37°C with shaking (200rpm) in 35mL cultures in MH broth to OD600=0.75, at which time they were split into 15mL cultures. One 15mL sample was treated with 4µg/mL chlorhexidine (0.5x MIC), whereas the other was not treated and used as a reference. Cultures were allowed to grow for a further 30 mins (to an average final OD600= ~1.35 for untreated cells and 1.25 for chlorhexidine treated samples), when cells were harvested by centrifugation and immediately suspended in Trizol reagent (Invitrogen). Total RNA was extracted using the PureLinkTM Micro-to-Midi Total RNA Purification kit (Invitrogen), incorporating an on-column DNAseI (Invitrogen) digestion.

overall_design: The experiment included using four grids of a custom Agilent 8 x 15000 spot microarray. Three biological replicates and one flip dye experiment.

middle: A

first: Ian

middle: T

last: Paulsen


title: Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein- Polysome gradient/microarray study

city: Toronto

first: Jason

middle: Gardiner

last: Dumelie

state: Ontario

address: 1 King's College Circle

department: Biochemistry

country: Canada

institute: University of Toronto

summary: To gain a panoramic view of Smaug function in the early embryo we identified mRNAs that are bound to Smaug using RNA co-immunoprecipitation followed by hybridization to DNA microarrays. We also identified the mRNAs that are translationally repressed by Smaug using polysome gradients and microarrays. Comparison of the bound mRNAs to those that are translationally repressed by Smaug and those that require Smaug for their degradation suggests that a large fraction of Smaug?s target mRNAs are both translationally repressed and degraded by Smaug. Smaug directly regulates components of the TRiC/CCT chaperonin, the proteasome regulatory particle and lipid droplets as well as many metabolic enzymes, including several glycolytic enzymes.

overall_design:
Embryos laid by wild-type or smaug1 homozygous mothers were collected 0-2 hours post-egglaying and lysed in an equal volume of polysome lysis buffer. The lysate was applied to polysome gradients that were fractionated into four fractions. mRNA was extracted from each fraction and converted to cDNA that was applied on custom-designed Nimblegen arrays. Three biological replicates were performed for each of the four fraction in  each of the two genotypes.
To demonstrate that the presence of mRNAs at the bottom of the gradient were the result of translation, we performed a puromycin experiment. smaug1 homozygous mothers were collected 0-2 hours post-egglaying and lysed in an equal volume of puromycin lysis buffer and then treated either with cycloheximide or puromycin. The lysate from each condition was applied to separate polysome gradients that were each fractionated into four fractions. mRNA was extracted from each fraction and converted to cDNA that was applied on custom-designed Nimblegen arrays. Two biological replicates were performed for each of the four fraction from each of the two conditions.

first: Linan

last: Chen

middle: G

first: Xiao

last: Li

first: Matthew

middle: H

last: Cheng

first: Zhiyong

last: Yang

first: John

middle: D

last: Laver

first: Najeeb

middle: U

last: Siddiqui

first: J

last: Westwood

first: Quaid

last: Morris

first: Howard

last: Lipshitz

first: Craig

last: Smibert


title: Dynamics of intercellular and extracellular (exosomal) miRNAs in hypoxic K562 cells

summary: Recently, the existence of extracellular miRNAs enclosed in exosomes has raised the possibility that they play an important role in cell-cell communication. To gain more insight into cell-cell communication via exosomal miRNAs, we investigated whether or not tumor cells exposed to hypoxia secrete exosomes which may affect angiogeneic activity. We used K562 cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from K562 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h were used for validation of angiogeneic activity, such as tube formation assay. The exosome secreted from K562 cells in hypoxic condition significantly enhanced tube formation by HUVECs when compared with exosome obtained from K562 cell in normoxic condition. To identify cellular and exosomal miRNAs universally responding to hypoxic condition, we assess the expression profiles of intercellular and extracellular miRNAs in K562 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA).

overall_design: K562 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).


city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

type: Methylation profiling by genome tiling array

summary: Genome-wide analysis of CHD8 binding sites as well as sites associated with the activating histone marks 2mk4H3 and 3mK4H3. These analyses have been performed by ChIP-chip using a custom microarray containing promoter regions and CpG islands. ChIP experiments were performed with the C33A human cervix carcinoma cell line.

overall_design: ChIP-chip analysis of CHD8, 2mK4H3 and 3mK4H3 in C33A cells

first: José

middle: I

last: Martín-Subero

middle: C


title: Dynamics of intercellular and extracellular (exosomal) miRNAs in hypoxic RPMI8226 cells

summary: Recently, the existence of extracellular miRNAs enclosed in exosomes has raised the possibility that they play an important role in cell-cell communication. To gain more insight into cell-cell communication via exosomal miRNAs, we investigated whether or not tumor cells exposed to hypoxia secrete exosomes which may affect angiogeneic activity. We used RPMI8226 cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from RPMI8226 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h were used for validation of angiogeneic activity, such as tube formation assay. The exosome secreted from RPMI8226 cells in hypoxic condition significantly enhanced tube formation by HUVECs when compared with exosome obtained from RPMI8226 cell in normoxic condition. To identify cellular and exosomal miRNAs universally responding to hypoxic condition, we assess the expression profiles of intercellular and extracellular miRNAs in RPMI8226 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA).

overall_design: RPMI8226 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).


title: Effects of domestication and GH transgenesis on mRNA profiles in rainbow trout

city: West Vancouver

first: Dionne

last: Sakhrani

state: BC

address: 4160 Marine Drive

institute: Fisheries and Oceans Canada

summary: Growth rate can be genetically modified in many vertebrates by domestication and selection, and more recently by transgenesis overexpressing growth factor genes (e.g. growth hormone, GH). While the phenotypic end consequence is similar, it is currently not clear whether the same modifications to physiological pathways are occurring in both genetic processes, nor to what extent they may interact when combined. To examine these questions, we have used rainbow trout as a model species because non-domesticated wild strains are available as comparators to assess genetic and physiological changes that have arisen from domestication and from GH transgenesis. In addition to pure wild and pure domesticated strains, two different GH transgenes with markedly different growth effects were examined, both in a wild background and in hybrids which combined domesticated and wild genomes in addition to the transgene. We find that liver mRNAs show highly concordant changes in levels in both types of fast-growing fish, relative to wild type, for both up- and down-regulated genes. Further, among domesticated, transgenic, and their hybrid genotypes, a strong positive correlation was found between growth rate and the number of genes affected or their levels of mRNA. Functional analysis found that genes involved in immune function, carbohydrate metabolism, detoxification, transcription regulation, growth regulation, and lipid metabolism were affected in common by domestication and GH transgenesis. The common responses of domesticated and GH transgenic strains is consistent with the GH pathway or its downstream effects being upregulated in domesticated animals during their modification from wild-type growth rates.

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design: Microarray analyses were performed on five individual rainbow trout per group of pure wild, pure domesticated, GH transgenic strain 1 in wild, GH transgenic strain 2 in wild,  GH transgenic strain 1 in wild-domestic hybrid, and GH transgenic strain 2 in wild-domestic hybrid hybridized (one slide per individual) against a common wild-type RNA pool.

first: Robert

last: Devlin

first: Samantha

middle: L

last: White

first: Ken

last: Overturf


title: Downregulation of specific miRNAs in hyperdiploid multiple myeloma mimics the oncogenic effect of IgH translocations occurring in the non-hyperdiploid subtype

city: Madrid

first: Ana

last: Rio-Machin

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Human Cancer Genetics

institute: CNIO

summary: Currently, multiple myeloma (MM) patients are broadly grouped into a non-hyperdiploid Group (nh-MM), highly enriched for IgH translocations, or into a hyperdiploid Group (h-MM), which is typically characterized by trisomies of some odd-numbered chromosomes.  We compared the miRNA expression profiles of these two groups and we identified 16 miRNAs that were downregulated in the h-MM group, relative to the nh-MM group. We found that target genes of the most differentially expressed miRNAs are directly involved in the pathogenesis of MM; specifically, the inhibition of hsa-miR-425, hsa-miR-152 and hsa-miR-24, which are all downregulated in h-MM, leads to the overexpression of CCND1, TACC3, MAFB, FGFR3 and MYC, which are the also the oncogenes upregulated by the most frequent IgH chromosomal translocations occurring in nh-MM. Importantly, we showed that the downregulation of these specific miRNAs and the upregulation of their targets also occur simultaneously in primary cases of h-MM. These data provide further evidence on the unifying role of cyclin C pathways deregulation as the key mechanism involved in the development of both groups of MM. Finally, they establish the importance of miRNA deregulation in the context of MM, thereby opening up the potential for future therapeutic approaches based on this molecular mechanism.

overall_design: miRNA expression profiling: The discovery series was composed of 53 CD138-positive de novo primary cases of Multiple Myeloma, of which 36 were classified as nh-MM and 17 as h-MM. Also included in this first analysis were 7 MM cell lines, six (JJN3, L363, OPM-2, K620, KMS28BM, KMS28PE) representing the nh-MM subtype and one (OH-2) as the model for h-MM. All samples, primary cases and cell lines, were labeled and hybridized in duplicate to the ‘8-pack’ Human miRNA Oligo Microarray G4470A (Agilent Technologies). We differentially expressed miRNA expression between the nh-MM and the h-MM subtypes were identified by standardized bioinformatics methods.

first: Bibiana

last: Ferreira

first: Travis

last: Henry

first: Gonzalo

last: Gómez-López

first: Xabier

last: Agirre

first: Sara

last: Alvarez

first: Sandra

last: Rodriguez-Perales

first: Felipe

last: Prosper

first: M

middle: J

last: Calasanz

first: Joaquín

last: Martínez

first: Rafael

last: Fonseca

first: Juan

last: Cigudosa


title: DNA copy number profiles of premalignant endobronchial lesions: a validated predictor for endobronchial cancer

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: Individuals who present with premalignant endobronchial lesions are considered at high risk of lung cancer. Nonetheless, premalignant lesions behave erratically and only a minority progresses towards lung cancer. Therefore, biomarkers need to be discovered that can aid in assessing an individual’s risk for subsequent cancer to better tailor treatment choices and avoid unnecessary follow-up procedures. We recently proposed a classifier of DNA copy number alterations (CNAs) at 3p26.3-p11.1, 3q26.2-29, and 6p25.3-24.3 as risk predictor for endobronchial cancer. The current study was set out to validate the classifier among an independent series of premalignant endobronchial lesions with various histological grades.   A series of 36 endobronchial premalignant lesions (8 squamous metaplasia, and 28 various grades of dysplasia) identified during autofluorescence bronchoscopy of 12 case subjects who had carcinoma in situ or carcinoma (≥CIS) during follow-up bronchoscopy at the initial site and 24 control subjects who remained cancer-free, was subjected to array Comparative Genomic Hybridization (arrayCGH). DNA copy number profiles were related to lesion outcome. Prediction accuracy of the previously defined molecular classifier to predict endobronchial cancer in this series was determined.   Unsupervised hierarchical clustering analysis revealed a significant association between cluster assignment and lesion outcome (p< 0.001), independent of histological grade, with quiescent profiles in controls (24/24) and aberrant profiles in the majority of cases (9/12). Our pre-defined classifier demonstrated 92% accuracy for predicting cancer outcome in the current sample series.   Our validated classifier holds great promise for stratification of patients with premalignant endobronchial lesions for risk of subsequent cancer.

overall_design: Fresh frozen specimens of 36 premalignant endobronchial biopsies. Test samples were compared to an external pool of normal male/female reference DNA.

last: van Boerdonk

first: Johannes

middle: M

last: Daniels

first: Peter

last: Snijders

first: Katrien

last: Grünberg

first: Erik

last: Thunnissen

first: Mark

last: van de Wiel

first: Bauke

last: Ylstra

first: Pieter

middle: E

last: Postmus

first: Egbert

middle: F

last: Smit

first: Gerrit

last: Meijer

first: Thomas

last: Sutedja

first: Daniëlle

last: Heideman


title: Developmental transitions of Coxiella burnetii grown in axenic media

status: Public on Dec 02 2013

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

summary: Coxiella burnetii undergoes a biphasic developmental cycle within its host cell that generates morphologically and physiologically distinct large cell variants (LCV) and small cell variants (SCV).  During the lag phase of the C. burnetii growth cycle, non-replicating SCV differentiate into replicating LCV that in turn differentiate back into SCV during stationary phase.  Nearly homogeneous SCV are observed in infected Vero cells after extended incubation (21 to 28 days). In the current study, we sought to establish whether C. burnetii developmental transitions in host cells are recapitulated during host cell-free (axenic) growth in first and second generation acidified citrate cysteine media (ACCM-1 and ACCM-2, respectively). We show that ACCM-2 supported developmental transitions and viability. Although ACCM-1 also supported SCV to LCV transition, LCV to SCV transition did not occur after extended incubation (21 days). Instead, C. burnetii exhibited a ghost-like appearance with bacteria containing condensed chromatin but otherwise devoid of cytoplasmic content. This phenotype correlated with a near total loss in viability between 14 and 21 days of cultivation. Transcriptional profiling of C. burnetii following 14 days of incubation revealed elevated expression of oxidative stress genes in ACCM-1 cultivated bacteria. ACCM-2 differs from ACCM-1 by the substitution of methyl-b-cyclodextrin (Mb-CD) for fetal bovine serum. Addition of Mb-CD to ACCM-1 at 7 days post-inoculation rescued C. burnetii viability and lowered expression of oxidative stress genes. Thus, Mb-CD appears to alleviate oxidative stress in ACCM-2 to result in C. burnetii developmental transitions and viability that mimic host cell-cultivated organisms. Axenic cultivation of C. burnetii in ACCM-2 and new methods

platform_organism:
Coxiella burnetii
Rickettsia rickettsii
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: Coxiella axenic media 1 vs 2

first: Kelsi

last: Sandoz

first: Daniel

first: Bryan

last: Hansen

first: Robert

last: Heinzen


title: Expresion analyses of red2 deletion cells

status: Public on Dec 01 2013

city: Tsukuba

first: Tomoyasu

last: Sugiyama

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary:
Investigation of whole genome gene expression level changes in red2∆, compared to the parental wild-type strain.
The red2 deletion cells analyzed in this study will be described in Sugiyama and Sugioka-Sugiyama.

overall_design: An mRNA profiling study using total RNA recovered from vegetatively growing wild-type culture of fission yeast and red2 deletion cultures of fission yeast.  Each chip measures the expression level of 4.997 genes from S.pombe with fourteen 60-mer probe pairs (PM/MM) per gene, with seven-fold technical redundancy.


title: Flutamide treated rat hepatocytes in microfluidic biochips

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: We investigated the effects of the flutamide (FLU) -induced liver injury in primary rat hepatocytes using our liver microfluidic biochips. Flutamide is used a non-steroidal anti-androgenic drug. Two flutamide concentrations, 10µM and 100µM, were used to expose the hepatocytes for 24h under perfusion.

overall_design: Primary rat hepatocytes were cultivated in microfluidic biochips and treated with 10 and 100µM of flutamide for 24h

first: Audrey

last: Legendre

first: Sebastien

last: Jacques

first: Eric

last: Leclerc


title: Induction of microRNA expression and processing via ERK/MAPK signaling during monocytic differentiation

city: Beijing

first: jing

last: wang

address: Tsinghu University

country: China

institute: Medical Systems Biology Research Center School of Medicine Tsinghua University

summary: This study produced a microarray-based screening for miRNAs responding to tetradecanoyl phorbol acetate (TPA) (for monocytic differentiation) treatment in various leukemia cell lines.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Using the microarray technique, global changes in miRNA expression after treatment of four leukemia cell lines (NB4, HL-60, U937 and K562) with TPA was profiled. This microarray chip contained 924 probes for 802 miRNAs from human, mouse and rat after discarding redundant sequences, and a further 122 predicted miRNA sequences from published data. To reduce individual variability, replicate array analysis used independently treated samples, and a technical replicate was also performed with the same sample.

first: Jing

last: Wang

first: Yuxiang

last: Zhou


title: Comparison of aCGH profiles from KB1(185stop)P, KB1(5382stop)P and KB1P mouse mammary tumors

first: Rinske

last: Drost

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

type: Genome variation profiling by genome tiling array

summary: While BRCA-related cancers respond well to double-strand break (DSB) inducing agents, resistance is a serious clinical problem. One mechanism of resistance is reversion of the BRCA1 mutation, suggesting that BRCA1 function is required for resistance. Here we show that secondary Brca1 mutations are not always necessary, since residual activity of the mutant BRCA1 protein can be sufficient for tumor cells to withstand treatment. Genomic profiling and RAD51 foci formation are currently seen as potential biomarkers to stratify patients for therapies targeting homologous recombination deficiency (HRD). However, we show that while mouse mammary tumors with different Brca1 mutations have identical genomic profiles, they respond considerably different to HRD targeted therapy. It may therefore be useful to stratify patients according to functional assays and the underlying BRCA1 mutation.

overall_design: We performed aCGH on mammary tumor DNA from KB1(185stop)P (n=20), KB1(5382stop)P (n=20) and littermate KB1P (n=22). Spleen DNA of the same animal was used as control material.

first: Kiranjit

middle: K

last: Dhillon

first: Ute

last: Boon

first: Eva

last: Schut

first: Ellen

last: Wientjens

first: Mark

last: Pieterse

first: Dafni

last: Chondronasiou

first: Hanneke

last: van der Gulden

first: Ingrid

last: van der Heijden

first: Christiaan

last: Klijn

first: Sjoerd

last: Klarenbeek

first: Liesbeth

last: van Deemter

first: Sven

last: Rottenberg

first: Peter

last: Bouwman

first: Toshiyasu

last: Taniguchi

first: Jos

last: Jonkers


title: affy_med_2012_03-Characterization of new phytostimulatrices molecules for the improvement of plants products and crop resistance to diseases

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary: affy_med_2012_03 - affy_med_2012_03 - Aphanomyces euteiches is a major legume parasite related to S. parasitica. Analysis of its cell wall showed the presence of an unsusual high content in GlcNAc, representing 10% of the total carbohydrates. Interestingly, this compound does not form crystalline chitin, but amorphous chitosaccharides. The aim goal of this study is to compare the response to a preparation of crab shell chitin chitooligosaccharides with a mean DP of 7 and to A.euteiches chitosaccharides at a transcriptomic level. This comparison will be done on Medicago truncatula wild type compared to the nfp-1 and nfp-2 mutants. -  7-day-old A17 wild type or mutant nfp-1 or nfp-2 plants were grown in vitro on liquid M medium. The entire roots were then treated (or not = controls) with a preparation of crab shell chitin chitooligosaccharides of a mean DP of 7 or with chitosaccharides from A. euteiches cell wall, names fraction P2F1, and harvested after 4 hours of incubation. Three independent repeats were performed.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 27 arrays - Medicago; normal vs ems mutant comparison

first: Marie-Béatrice

last: Bogeat-Triboulot

first: Stephanie

last: Huguet

first: ARNAUD

last: BOTTIN

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Leukocyte CD antibody microarray profiling reveals immune markers associated with aging and gender (datasets 1 and 2)

city: Boston

first: Joshua

middle: WK

last: Ho

state: MA

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

summary: The study of disease-associated immune biomarkers has revealed underlying pathogenic mechanisms and provided diagnostic and prognostic values in numerous clinical settings. Accurate immune profiling of normal age and sex demographics is crucial for understanding the relevance of disease biomarkers. The incidence of age-associated diseases in the elderly and prevalence of diseases in specific genders may be explained by these normal phenotypic variation in the cellular immune system. Here we use microarrays of cluster of differentiation (CD) antibodies to immunophenotype populations of peripheral blood mononuclear cells (PBMCs) from healthy adult blood donors. The data revealed a set of statistically significant age- and gender-dependent expression patterns across the study population. We identified functional differences in immune biomarkers on PBMC associated with major innate, adaptive and inflammatory immune functions. The CD array data supported established observations using flow cytometric methods on age-associated changes in immune biomarkers, while also identifying novel markers associated with age and/or gender. The data demonstrates the utility of CD antibody arrays in providing a systematic and quantitative basis for understanding the development and progression of diseases that have an age-dependent and gender-specific etiology.

overall_design: Blood samples were collected from healthy male and female blood donors acrooss various age groups, predominantly Caucasians, from the Australian Red Cross Blood Service, Sydney, Australia, and from elderly males enrolled in the Concord Health and Aging in Men Project (CHAMP) at Concord Hospital, Sydney, Australia. PBMCs were fractionated from whole blood and applied to a cell capture CD antibody microarray. The microarray was then scaned by a  DotScan™ slide reader (Medsaic; Eveleigh, NSW, Australia). The number of immobilized cells was proportional to the light scattered at each antibody spot. Binding of PBMCs to each antibody dot was monitored by light scatter and averaged between the duplicate spots on each slide. We then performed statistical analysis to identify CD antigen markers that has an statistically significant association with age and/or gender

middle: W

first: Alana

middle: N

last: Mohamed

first: Cristobal

last: dos Remedios

first: Wayne

middle: B

last: Dyer


title: Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen.

status: Public on Nov 25 2013

city: Turku

first: Sini

last: Junttila

address: Tykistökatu 6 A

department: Centre for Biotechnology

country: Finland

institute: University of Turku

summary: We have utilized the raw sequence data from our earlier investigation of the lichen transcriptome to design a custom DNA microarray for C. rangiferina in order to study the transcripts expressed in lichen thallus during dehydration and rehydration. The aim of this study was to identify the genes most differentially expressed during the rehydration and drying processes and also to get a more integrative view of the molecular players who may play roles in the processes required for lichen desiccation tolerance and the rapid re-establishment of photosynthesis through functional annotation.

overall_design: 8 samples with three biological replicates for each sample, altogether 24 samples. D1h samples have been drying for 1 hour, D3h samples for 3 hours, D6h samples for 6 hours and Dry samples for 24 hours. W15m samples have been wetted for 15 minutes, W30m samples for 30 minutes, W1h samples for 1 hour and Wet samples for 3 hours.

first: Asta

last: Laiho

first: Attila

last: Gyenesei

first: Stephen

last: Rudd


title: Transcriptional profiling of UV-B response of Populus alba.

city: Florence

first: Giovanni

last: Emiliani

address: via S. Bonaventura, 13

department: Dept. of Environmental and Forestry Technologies and Sciences

institute: University of Florence

summary:
Microarray technology was used to assess transcriptome changes in poplar (Populus alba L.) under a realistic simulation of increased UV-B radiation. Plants were UV-Bbe (UV-B biologically effective radiation) supplemented with a dose of 6 kJ/m2/day for 12 hours per day and allowed to recover during the night. Poplar plants were UV-B treated using a refined controlled environment able to guarantee a realistic simulation of natural conditions, especially for light parameters such as presence of background UV-B radiation for control plants and balanced PAR/UV-A/UV-B ratio. A time course experiment was planned to look both at the rapid and delayed response of poplar to UVB; two time points after 3 h (T3h) and 30 h (6th hour of the third day of treatment, T30h) were considered. 4 independent biological replicates were analysed for each time point. Competitive hybridisations were carried out using the PICME 28K microarray.
Keywords: Time course experiment, stress response

platform_organism:
Populus trichocarpa x Populus deltoides
Populus euphratica
Populus tremula x Populus alba

overall_design: Two condition experiment: UVB supplemented plants vs normal UV-B level plants. Biological replicates: 4 UVB suplemented plants, 4 control plants, two time points, one replicate per array. Dye swap between replicates.

first: Nathaniel

middle: R

last: Street

first: Donatella

last: Paffetti

first: Gail

last: Taylor


title: Transcriptome analysis of Traf6 function in early zebrafish embryogenesis

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

institute: AMC

summary: In order to study Traf6 function during early zebrafish embryogenesis, transcriptome expression profiling was performed at 30% epiboly using a morpholino based knock-down approach.

overall_design: Two-factorial design with the factors 'Treatment' (5 levels:'Phenol Red', 'Standard Control', 'Mismatch', 'Morpholino1' and Morpholino 2') and 'Dose' (3 levels: 'Low', 'Middel' and 'High') with the factor 'Dose' only being applicable to the morpholino injections and not to the 'Phenol Red' control.

first: O

first: H

last: Rauwerda

first: M

last: Jonker

first: F

last: Wittink

first: T

last: Breit

first: A

middle: H

last: Meijer

middle: P

last: Spaink


title: ATM-dependent Transcriptional Responses to 1.5 Gy Gamma Radiation in Human Lymphocytes

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Ataxia telangiectasia (AT) is an autosomal recessive disorder characterized by neuronal degeneration, telangiectasias, acute cancer predisposition, and hypersensitivity to ionizing radiation (IR).  The gene defective in AT, ATM (for AT-mutated), encodes a protein, pATM that has been found to have IR-inducible kinase activity.  Cells from individuals with AT exhibit severely attenuated cell cycle checkpoints in response to gamma radiation exposure.  pATM has been hypothesized to act as part of a complex that senses DNA damage, in particular, DNA double strand breaks.  We are studying the pATM-dependent gene expression responses to a dose of 1.5 Gy radiation in lymphoblastoid cell lines from multiple individuals with either wild type or mutated ATM.  The gene expression analyses were performed on Agilent Human 1A Oligo chips containing approximately 16,000 60mer probes.  We identified a set of genes whose gene expression changes are ATM-dependent following exposure to 1.5 Gy IR.  This set of genes was tested by real time quantitative PCR analysis.

overall_design: The study consists of one dose group - 1.5 Gray gamma radiation.  Samples were collected 6 hr following irradiation (treated) or mock irradiation (controls) for each culture.  Each culture has a treated sample and a control sample.  There are cultures from 6 wild-type ATM individuals and cultures from 6 individuals that are ATM-deficient, for a total of 12 cultures.  Hybridizations compared RNA extracted from each individual culture's treated sample against its corresponding control sample, and were performed as dye-flip duplicates (1 replicate in each direction).  Hybridizations were performed on the Human 1A Oligo Chips using low input, direct labeling at Paradigm Genetics Laboratory.  Microarray scanning was performed with the Agilent G2565AA Scanner.  Paradigm Standard Operating Procedures were followed for quality analysis, sample labeling, microarray hybridization and washing, scanning, image analysis and initial data analysis.

first: Cynthia

last: Innes

first: Richard

middle: S

last: Paules

first: Tong

last: Zhou

first: William

last: Kaufman


title: Gene signature predictive of response to chemotherapy in mCRC [RT-PCR]

status: Public on Nov 20 2013

city: Seville

first: Purificacion

last: Estevez-Garcia

state: Seville

address: Manuel Siurot avenue

department: Molecular Oncology

institute: Institute of Biomedicine

summary: The objective is to generate a robust and validated predictor profile for chemotherapy response in patients with mCRC using microarray gene expression profiles of primary colorectal cancer tissue.

overall_design:
To define a gene signature of response to chemotherapy in metastatic colorectal cancer, samples were obtained from 40 patients from Marques de Valdecilla Hospital who underwent primary surgery. Gene expression was detected and quantified using the Human Whole Genome U133 Plus 2.0 array (Affymetrix), containing 54675 human gene probes. The validation set consisted of 119 samples from Hospital Virgen del Rocio, Seville, Spain; Hospital Virgen de la Victoria, Malaga, Spain; Hospital de la Merced, Osuna, Spain and Hospital Marqués de Valdecilla, Santander, Spain, and included 86 tumor samples (40 coming from the training set and 46 from newly treated CRC patients) and 33 normal tissue samples of CRC patients used as controls. Custom-designed TaqMan® Low Density Arrays (TLDA) 7900 HT Micro Fluidic Cards including the 161 genes selected for validation were run and analyzed by the ABI PRISM® 7900HT Sequence Detection System (SDS 2.2, Applied Biosystems) according to manufacturer's protocol (Applied Biosystems). Expression of target miRNAs was normalized in relation to the expression of GAPDH.  Cycle threshold (Ct) values were calculated using the SDS software v.4.2 using automatic baseline settings and a threshold of 0.2. Relative quantification of gene expression was calculated by the 2−ΔCt method (Applied Biosystems user bulletin no. 2 (P/N 4303859)).

This submission represents the RT-PCR component of the study only

first: Sonia

last: Molina-Pinelo

first: Marta

last: Benavent-Viñuales

first: Fernando

last: Rivero

first: Javier

last: Gomez

first: Maria

middle: D

last: Pastor

first: Amancio

last: Carnero

first: Luis

last: Paz-Ares

first: Rocio

last: Garcia-Carbonero


title: Differential gene expression during cold-acclimation in barley, wheat and rye

status: Public on Nov 30 2013

city: Gatersleben

first: Athmer

last: Benedikt

address: Correnstrasse 3

country: Germany

institute: IPK Gatersleben

summary: The present transcript profiling compares the gene expression during cold-acclimation in different genotypes of  barley (Hordeum vulgare L.), wheat (Triticum aestivum L.) and rye (Secale cereale L.) in order to determine factors influencing frost tolerance. Because of its outstanding robustness against adverse environmental conditions rye is considered to be a model species for abiotic stress tolerance. Wheat is moderate frost-tolerant and barley is most sensitive species in this study. The aim of this study elucidate conserved,  as well as, species-specific gene regulation across the Triticeae. Furthermore, transcript abundances were correlated between the distinct frost tolerances of genotypes within each species in order to find candidate genes for frost tolerance.

sample_organism:
Hordeum vulgare
Secale cereale
Triticum aestivum

overall_design: Six winter-genotypes of each species with variable frost toleance (3 sensitive, 3 tolerant) were selected and cold-acclimated at 2°C under phytotron conditions. Sampling was done in the middle of photo period at day 0 (control), day 1, day 7 and day 21 of cold-acclimation. RNA's extracted from primary shoots of three biological replications were pooled. Cross-species transcript profiling was applied by using a barley unigene cDNA-macroarray comprising more than 12000 features, spotted in duplicate.

first: Benedikt

last: Athmer

first: Gabor

last: Kocsy

last: Galiba

first: Patrick

last: Schweizer

first: Fruzsina

last: Szira

first: Nils

last: Stein


title: DamID profiling of neural transcription factor (Abrupt and Knot) binding in Drosophila melanogaster embryos

status: Public on Nov 27 2013

city: Kyoto

first: Yukako

last: Hattori

address: Sakyo-ku

department: Graduate School of Biostudies

institute: Kyoto University

type: Genome binding/occupancy profiling by genome tiling array

summary: Paper abstract: The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively. We performed binding-site mapping and transcriptional profiling of isolated these neurons. Their profiles were similarly enriched in cell-type-specific enhancers of genes implicated in neural development. We identified a total of 429 target genes, of which 56 were common to Ab and Kn; these targets included genes necessary to shape dendritic arbors in either or both of the two sensory subtypes. Furthermore, a common target gene, encoding the cell adhesion molecule Ten-m, was expressed more strongly in class I than IV, and this differential was critical to the class-selective directional control of dendritic branch sprouting or extension. Our analyses illustrate how differentiating neurons employ distinct and shared repertoires of gene expression to produce class-selective morphological traits.

overall_design: Each Dam-fusion-derived sample is compared to a control Dam-only sample. Four biological replicates were performed.

first: Tadao

last: Usui

first: Daisuke

last: Satoh

first: Sanefumi

last: Moriyama

first: Kohei

last: Shimono

first: Takehiko

last: Itoh

first: Katsuhiko

last: Shirahige

first: Tadashi

last: Uemura


title: Gene expression profile of a S. cerevisiae strain deleted in CSN5/RRI1 gene (systematic name YDL216C)

status: Public on Oct 23 2013

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary:
The COP9 signalosome (CSN) is a highly conserved eukaryotic protein complex which regulates the Cullin-RING family of ubiquitin ligases and carries out a deneddylase activity that resides in subunit 5 (CSN5). The budding yeast CSN is biochemically active and deletion mutants of each of its subunits exhibit deficiency in deneddylation of cullins, although the biological context of this activity is still unknown in this organism.
To further characterize CSN function in budding yeast, we present here a transcriptomic analysis of a S. cerevisiae strain deleted in CSN5/RRI1 gene (hereafter referred to as CSN5), coding for the only canonical subunit of the complex. We show that Csn5 is involved in the modulation of the genes controlling aminoacid and lipid metabolism, and especially ergosterol biosynthesis. These alterations in gene expression correlate with the lower ergosterol levels and increased intracellular zinc content which we observed in csn5 null mutant cells.

overall_design: Two biological replicates, csn5 deleted strain vs. isogenic wild-type strain W303

first: Chiara

last: Salvi

first: Virginia

last: De Cesare

first: Rodolfo

last: Negri


title: Transcriptomes of Rice internode before and after heading

status: Public on Oct 01 2013

city: Nagoya

first: Ko

last: Hirano

state: Aichi

address: Furo-cho Chikusa-ku

institute: Nagoya University

summary: To identify genes that co-express with rice cellulose synthase genes involved in rice secondary cell wall formation, transcriptome analyses was performed using rice internodesbefore and after the heading stage, where secondary cell wall formation extensively occur.

overall_design:
Transcriptomes of rice third or the fourth internodes were analyzed at 17, 8, and 1 day before, and 6, 13, and 35 days after heading
Please note that the current data were normalized together with additional 143 sample data available in GEO and the list of the sample accessions is provided in Series supplementary file [normalized_together_GSMs.txt].

first: Makoto

last: Matsuoka

first: Koichiro

last: Aya

first: Yoichi

last: Morinaka

first: Shiro

last: Nagamatsu

first: Yoshiaki

last: Nagamura

first: Yutaka

last: Sato

first: Baltazar

middle: A

last: Antonio

first: Nobukazu

last: Namiki


title: Novel single nucleotide polymorphism markers for low dose aspirin-associated small bowel bleeding

status: Public on Nov 08 2013

city: Osaka-Sayama

first: Yoshihiko

last: Fujita

address: 377-2 Ohno-Higashi

institute: Kinki university School of Medicine

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

summary: Blood from 17 patients taking enteric-coated low-dose aspirin (LDA) and with suspected bleeding from small intestine and 18 control patients taking aspirin were analyzed. Results provide insight into the risk for aspirin-induced small bowel bleeding.

overall_design: 35 samples; 1 array per sample.

first: Akiko

last: Shiotani

first: Takahisa

last: Murao

first: Kazuto

last: Nishio

first: Yoshinori

last: Fujimura

first: Takashi

last: Sakakibara

first: Ken

last: Haruma


title: Rice gene expression using Agilent custom 8X60K Microarray

status: Public on Oct 18 2013

city: Singapore

first: Shu-Ye

last: Jiang

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory, National University of Singapore

summary: We designed an array based on the release 7 of Michigan State University (MSU) rice genome annotation database (http://rice.plantbiology.msu.edu). The array was used for investigating the expression divergence and regulation between two contrasting rice genotypes under high salinity stress.

overall_design: The expression analysis was carried out using 14-day old whole seedlings from both japonica and indica rice lines. Two samples from NaCl treatment (0h and 8h) for each line were collected for the analysis. Two biological replicates were carried out for both control and NaCl treatments, resulting in a dataset of 8 microarrays.

first: S

first: A

last: Ma

first: R

last: Ramamoorthy

last: Ramachandran


title: 3D Expression Data of Myc and Myc phospho-mutants

status: Public on Sep 24 2013

city: Toronto

first: Michelle

last: Chan-Seng-Yue

address: 101 College Street

institute: Ontario Institute for Cancer Research

summary: We sought to examine the mechanism through which phospho-mutants can contribute to the transformation of MCF10A acini. To investigate this, we examined the RNA abundance of Myc and Myc phospho-mutants (T58A, S71A/S81A, and Myc-4A) against a GFP control.

overall_design: Three independent biological replicates of the five samples (Myc, T58A, S71A/S81A, Myc-4A and GFP control) were isolated on day 4 and processed on Affymetrix HG-U133 Plus2 chips.

first: Amanda

last: Wasylishen

first: Chrstina

last: Boss

first: Dharmendra

last: Dingar

first: William

last: Tu

first: Manpreet

last: Kalkat

first: Pak-Kei

last: Chan

first: Peter

last: Mullen

first: Ling

last: Huang

first: Natalie

last: Meyer

first: Senthil

last: Muthuswamy

first: Brian

last: Raught

first: Linda

middle: Z

last: Penn


title: Pinus massoniana Transcriptome Responses Involved in Phosphorus Deficiency

city: Guiyang

first: Fuhua

last: Fan

address: Xiahui Street, Huaxi

institute: Guizhou University

summary: Masson pine (Pinus massoniana) has evolved some adaptations for growth in low P soils. To elucidate these mechanisms, we investigated global gene expression profiles of the masson pine responding to long-term phosphorus starvation and different Pi levels (P1, 0.01 mM P; P2, 0.06 mM P).

overall_design: Analysis used phosphorus-sufficient treatment RNA as control samples for comparison to the experimental samples (P1 and P2) taken at 12, 24, 48 and 60 day. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.

first: Xiaopeng

last: Wen


title: Regulation of gene expression by Candidatus Liberibacter asiaticus in stem and root of Sweet orange (Citrus Sinensis)

city: Lake Alfred

first: Valente

last: Aritua

state: Florida

address: 700 Experiment Staion Road

department: Plant Pathology

institute: University of Florida

summary:
Candidatus Liberibacter asiaticus infection of citrus is characterized by symptom variability within and among organs. In order to identify molecular processes involved in the regulation of organ response to Ca. Liberibacter infection, the gene expression patterns in C. sinensis leaf, stem, and root was examined in Affymetrix microarray.
Our analyses showed that Ca. L. asiaticus reprograms several cellular and metabolic processes in C. sinensis, with most categories regulated in leaves, followed by stems and least in roots. Among them, we identified genes whose expression is regulated in organ-specific manner, reflecting organ specialization in the molecular response to Ca. L. asiaticus.
Differences in gene expression were expected between these organs because of functional divergence among them.

overall_design: Two-year old Valencia sweet orange (C. sinensis) plants were graft inoculated with budwood from Ca. L. asiaticus-infected citrus plants. Successful infection of the inoculated plants was confirmed in both conventional and quantitative PCR with specific primers to Ca. L. asiaticus.  The stem and root samples used for RNA extraction and hybridization on Affymetrix microarrays were obtained from three symptomatic and three healthy control trees of similar size, 16 months after the inoculation.

first: Nain

last: Wang


title: Nucleosome free DNA- and acetyl histone-binding components recruit SWR1 to yeast promoters for H2A.Z replacement

status: Public on Sep 16 2013

city: Bethesda

first: Anand

last: Ranjan

state: Maryland

address: 37 convent st, room 6114

department: LBMB

institute: NCI

summary: The histone variant H2A.Z is a genome-wide signature of nucleosomes proximal to eukaryotic regulatory DNA. While the multi-subunit SWR1 chromatin remodeling complex is known to catalyze ATP-dependent deposition of H2A.Z, the mechanism of recruitment to S. cerevisiae promoters has been unclear. A sensitive assay for competitive binding of di-nucleosome substrates revealed that SWR1 preferentially binds long nucleosome-free DNA adjoining core particles, allowing discrimination of gene promoters over gene bodies. We traced the critical DNA binding component of SWR1 to the conserved Swc2/YL1 subunit, whose activity is required for both SWR1 binding and H2A.Z incorporation in vivo. Histone acetylation by NuA4 enhances SWR1 binding, but the interaction with nucleosome-free DNA is the major determinant. ‘Hierarchical cooperation’ between high affinity DNA- and low affinity histone modification-binding factors may reconcile the large disparity in affinities for chromatin substrates, and unify classical control by DNA-binding factors with post-translational histone modifications and ATP-dependent nucleosome mobility.

overall_design: Swr1 TAP IF of various mutants

first: A

first: G

last: Mizuguchi

first: P

last: Fitzgerald

first: C

last: Wu


title: Expression data from endthelial cells in ductus arteriosus and aorta in rat fetuses or neonates

city: Shinjuku-ku

first: Norika

middle: Mengchia

last: Liu

address: 2-2, Wakamatsu-cho

department: Dep. Life science & Medical Bioscience

institute: Waseda University

summary:
Endothelial cells (Ecs) lining the blood vessels have been known to have a variety of functions and play a central role in homeostasis of the circulatory system.
Since ductus arteriosus (DA) has unique characteristics comparing other vessels, we hypothesized that ECs were the primary target to investigate the molecular mechanisms of DA-specific vasoconstriction and vascular remodeling.

overall_design: Using fluorescence activated cell sorter, we isolated ECs from pooled tissues from the DA or the aorta of Wistar rat fetuses on the 21st day of gestation (e21) or 30 minutes after birth (day0). We prepared 3 sets of ECs in each tissues and time points. We aimed to compare the gene profiles of DA and the aorta at each developmental stage.

first: Tomohiro

last: Yokota

first: Susumu

last: Minamisawa


title: Different DNA methylation between hypothalamus paraventricular (PVH) and ventromedial (VMH) nuclei

city: Houston

first: Ge

last: Li

state: TX

address: 1100 Bates St.

department: Pediatrics

institute: Baylor College of Medicine

summary: The goal is to compare the DNA methylation patterns between ARH and PVH to examine to what extent DNA methylation is region specific in genome scale.

overall_design: ARH and PVH were micro-dissected from mice brains. Each 7 pieces of ARH or PVH were pooled and used for DNA methylation comparison by methylation specific amplification microarray (MSAM). As a brief description of the MSAM: 500ng of genomic DNA was serially digested with SmaI and XmaI followed by an adaptor ligation and adaptor mediated PCR amplification and then cohybridization. Two-color cohybridizations were performed as paired comparison of PVH vs. ARH with two biological replicates including dye swap.

first: Wenjuan

last: Zhang

first: Natalia

last: Matalan-Hung

first: Richard

last: Simerly

first: Robert

last: Waterland


title: Time series of Methanococcus maripaludis MM901, a shift from a H2-limited condition to a H2-excess condition

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

type: Expression profiling by genome tiling array

summary: Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. maripaludis through integrated analysis of the transcriptome structure and a newly constructed Peptide Atlas. The environment and gene-regulatory influence network (EGRIN) model of the strain was constructed from a compendium of transcriptome data that was collected over 100 different steady-state and time course experiments that were performed in chemostats, or batch cultures, under a spectrum of environmental perturbations that modulated methanogenesis. We discovered that at least five regulatory mechanisms act in a combinatorial scheme to inter-coordinate key steps of methanogenesis with different processes such as motility, ATP biosynthesis, and carbon assimilation. Through a combination of genetic and environmental perturbation experiments we have validated the EGRIN-predicted role of two novel TFs in the regulation of phosphate-dependent repression of formate dehydorgenase – a key enzyme in the methanogenesis pathway.

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009).   Growth conditions were carefully designed to separate the effects of different environmental factors. To ensure physico-chemical factors being constant, all cell cultures were performed using continuous cultivations with a constant dilution rate. The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). For shifts from a H2 excess to a H2 limited condition, H2 was lowered from standard 110 mL/min to 21 mL/min and Ar was raised from standard 35 mL/min to 125 mL/min. The dilution rate was held constant at 0.083 h-1. For time-series array data, cultures before perturbation were allowed to reach steady state. We rapidly changed concentration(s) of H2 and/or a nutrient, and sampled at intervals after the perturbation; right away, after 5 mins, 10, 20, 30, 45, 60, 90, 120, 180, and 300 mins. Culture samples (1.5 mL) were rapidly removed from the chemostat vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.

first: Sung-Ho

first: June

last: Burn

first: Min

last: Pan

first: John

last: Leigh

first: Nitin

last: Baliga


title: MicroRNA-146 function in the innate immune response of zebrafish embryos to Salmonella typhimurium infection [miRNA profile]

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

institute: Institute of Biology, Leiden University

summary: This study reports on  infection-inducible miRNAs in zebrafish. Using a custom-designed microarray platform for miRNA expression we found that miRNAs of the miR-21, miR-29, and miR-146 families were commonly induced by infection of zebrafish embryos with Salmonella typhimurium and by infection of adult fish with Mycobacterium marinum.

overall_design: A custom-designed Agilent zebrafish 8x15k miRNA platform was used to profile miRNA  expression in zebrafish embryos infected with Salmonella typhimurium strain SL1027 and adult zebrafish infected with Mycobacterium marinum strain Mma20 . The 15k design contained a duplicate of 7604 probes of 60-oligonucleotide length. The probes consisted of 2x22 nucleotide sequences antisense to mature miRNAs separated by a spacer of 8 nucleotides (CGATCTTT) and with a second spacer with the same sequence at the end. From 7604 probes 546 were designed for left (5') and right (3') arms of the hairpins of zebrafish miRNAs  known in miRBase, while the remainder 7058 probes corresponded to predicted hairpin structures in the zebrafish genome that might include additional miRNAs but were not considered in this study. Zebrafish embryos were infected at 28 hours post fertilization (hpf) by injecting 200-250 colony forming units of Salmonella typhimurium into the caudal vein and miRNA profiles of infected embryos were compared to control embryos injected with PBS (phosphate buffered saline) at 8 hours post-infection (hpi; 3 biological replicates and 2 technical replicates per each sample). Adult zebrafish were infected with 10000 colony forming units of Mycobacterium marinum and miRNA profiles were compared to PBS-injected control fish at 6 days post infection (dpi; 3 biological replicates). For dual color hybridization of the Agilent chips miRNA samples from infected zebrafish were labeled with Hy3 and samples from control fish were labeled with Hy5.

first: Zakia

last: Kanwal

first: Anita

last: Ordas

first: Valesca

last: Lindenberg

first: Matyas

last: Mink

first: Herman

last: Spaink


title: Role of the ArcAB two-component system in oxidative stress

status: Public on Sep 18 2013

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: Salmonella enterica serovar Typhimurium  is  a  Gram-negative  bacterium,  facultative anaerobe and  intracellular  pathogen  that  causes  enteric  fever  in  mice.  Once  orally  ingested, Salmonella  invades  and  traverse  the  mucosal  intestinal  epithelia,  where  it  is  phagocytized  by specialized  cells  including macrophages,  dendritic  cells  and  neutrophils. Within  these  cells,  the bacterium is kept in a compartment termed Salmonella containing vacuole where it is exposed to different adverse conditions including nutrient deprivation, acid pH, reactive oxygen (ROS) as well as nitrogen (RNS) species and low oxygen levels. Among the signals encountered by the bacteria, oxidative stress is one of the main challenges that it has to overcome in order to survive. In this context,  the OxyR  and SoxRS  proteins  are  the most  studied  regulators  involved  in  response  to ROS.  However,  in  the  past  years  growing  evidence  suggests  that  the  ArcAB  two-component system might play a key  role  in modulating gene expression  in response  to  ROS.  Furthermore,  the  global  regulator  ArcA  is  required  for  the  resistance  of Escherichia  coli, S.  Enteritidis and Typhimurium to hydrogen  peroxide  (H2O2), however, the ArcA regulon under oxidative stress conditions remains elusive. Therefore, the aim of this work was to demonstrate that ArcAB regulates the expression of genes in response to hydrogen peroxide and determine the ArcA regulon under this condition. To achieve this, we evaluated transcriptomic changes in strain 14028s, ∆arcA in response to H2O2.

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

overall_design: Total RNA was harvested from three biological replicates of wt and arcA mutant cultures exposed or unexposed to 1.5 mM hydrogen peroxide for 20 min in LB medium.

first: Eduardo

last: Morales

first: Steffen

last: Porwollik

first: Prerak

last: Desai

first: Claudia

last: Saavedra


title: Effect of different Two-component systems system deletion in S. aureus NCTC8325

status: Public on Sep 30 2013

city: He Fei

first: Haipeng

last: Sun

state: An Hui

address: Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: To analyze function of three Two-component systems SAOUHSC_00184-185, SAOUHSC_01313-1314, and SAOUHSC_01980-1981, we have employed whole genome microarray expression profiling to identify genes transcription changed in respective mutant strains. Target TCSs were replaced by ermB gene.

sample_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: Cells were grown to OD600=2.0, and the RNA level of wild type NCTC8325 and three TCSs mutant were compared.

first: Yifan

last: Yang


title: In search of epigenetic marks in testes and sperm cells of differentially fed boars [Agilent]

city: Berne

first: Martin

last: Braunschweig

state: Berne

address: Bremgartenstrasse 109A

department: Vetsuisse Faculty

country: Switzerland

institute: University of Bern

summary: We investigated the nutritional effects on gene expression in testes of F0 boars from a three generation Large White pig feeding experiment. A group of experimental (E) F0 boars were fed a standard diet supplemented with high amounts of methylating micronutrients whereas a control (C) group of F0 boars received a standard diet. These differentially fed F0 boars sired F1 boars which then sired 60 F2 pigs which were investigated in a previous study. The aim of this project was to investigate if the nutrition affects gene expression in testis of differentially fed boars and thus impact on spermatogenesis. We found a small number of 70 genes that were differentially expressed (fc ≥ 1) on the P<0.01 significance level. The false discovery rate (FDR) was 0.82 indicating that only a small portion of these genes are real positives. Nevertheless, we performed a pathway analysis and found this moderate differential expression associated with pathways maps of development_A2B receptor: action via G-protein alpha s, cell adhesion_Tight junctions and cell adhesion_Endothelial cell contacts by junctional mechanisms. The gene ontology (GO) processes that matched the gene expression data in boars’ testes were positive regulation of nucleobase-containing compound metabolic process, cellular response to hormone stimulus and cellular process. The pathway maps and GO processes associated with gene expression differences do not indicate a simple relationship between nutritional influences and gene expression in testes. Nevertheless the Adenosine A2B receptor influences cell differentiation and proliferation and has thus far reaching consequences. Similar applies to those GO processes positive regulation of nucleobase-containing compound metabolic process, cellular response to hormone stimulus and cellular process that were associated with differentially expressed genes between the testes samples. The expression result is thus not conclusive of whether the diet affects processes related to transmittable epigenetic marks. The results, however, indicate that the extreme supplementation of methylating micronutrients from month one to month ten of age has a very moderate (if any) effect on gene expression in boar testes as measured by microarray analysis.

overall_design: Gene expression in testes from differentially fed F0 boars was measured. F0 boars received either a standard diet or a standard diet supplemented with methylating micronutrients. These boars were used to study transgenerational epigenetic inheritance in a three generation pig pedigree. Therefore it was of interest if the diet affects gene expression in testes and so could impact spermatogenesis.

first: Rémy

last: Bruggmann

first: Vidhya

last: Jagannathan


title: Genome-wide EMSA (gEMSA) of ORC and yeast genomic DNA

city: Madison

first: Catherine

middle: Anne

last: Fox

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin - Madison

summary: Eukaryotic DNA replication origins are selected in G1-phase when the origin recognition complex (ORC) binds chromosomal DNA, triggering a series of molecular events that culminate in the initiation of DNA replication (a.k.a. origin firing) during S-phase. Each chromosome requires multiple origins for its duplication, and each origin fires at a characteristic time during S-phase, creating a cell-type specific genome replication pattern with relevance to differentiation, genome stability and evolution. It is unclear whether ORC-origin interactions are relevant to the regulation of origin activation time. Here we applied a novel genome-wide strategy to classify origins in the model eukaryote Saccharomyces cerevisiae based on the types of molecular interactions used for ORC-origin binding. Specifically, origins were classified as DNA-dependent when the strength of ORC-origin binding in vivo could be explained by the affinity of ORC for origin DNA in vitro, and, conversely, as ‘chromatin-dependent’ when the ORC-DNA interaction in vitro was insufficient to explain the strength of ORC-origin binding in vivo. The two classes of origins were distinct in terms of local nucleosome architecture and dependence on origin-flanking sequences in plasmid replication assays, consistent with local features of chromatin promoting ORC binding at ‘chromatin-dependent’ origins. Importantly, origins that fired in late S-phase, but not those that fired in early S-phase, showed a significant dependence on the ORC-origin DNA interaction for ORC binding in vivo. Therefore we demonstrate for the first time a connection between ORC-origin binding mechanisms and the regulation of origin activation time at a genome-wide level.

overall_design: Analysis of ORC genomic DNA binding across three ORC concentrations.

first: Timothy

last: Hoggard

first: Erika

last: Shor

first: Carolin

last: Muller

first: Conrad

last: Nieduszynski


title: Time series of Methanococcus maripaludis MM901:del_mtd (MMP0372), a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)

first: Sung Ho

last: Yoon

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009).   Growth conditions were carefully designed to separate the effects of different environmental factors. To ensure physico-chemical factors being constant, all cell cultures were performed using continuous cultivations with a constant dilution rate. The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). For shifts from a H2 excess to a H2 limited condition, H2 was lowered from standard 110 mL/min to 21 mL/min and Ar was raised from standard 35 mL/min to 125 mL/min. For shifts from P-limited to P-excess conditions, phosphate was raised from 0.12 mM to the standard 0.8 mM. The dilution rate was held constant at 0.083 h-1. For time-series array data, cultures before perturbation were allowed to reach steady state. We rapidly changed concentration(s) of H2 and/or a nutrient, and sampled at intervals after the perturbation; right away, after 5 mins, 10, 20, 30, 45, 60, 90, 120, 180, and 300 mins. Culture samples (1.5 mL) were rapidly removed from the chemostat vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.

first: Sung-Ho

first: June

last: Burn

first: Min

last: Pan

first: John

last: Leigh

first: Nitin

last: Baliga


title: Time series of Methanococcus maripaludis MM901, a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)


title: Time series of Methanococcus maripaludis MM901:del_MMP1100, a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009).   Growth conditions were carefully designed to separate the effects of different environmental factors. To ensure physico-chemical factors being constant, all cell cultures were performed using continuous cultivations with a constant dilution rate. The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). For shifts from a H2 excess to a H2 limited condition, H2 was lowered from standard 110 mL/min to 21 mL/min and Ar was raised from standard 35 mL/min to 125 mL/min. For shifts from P-limited to P-excess conditions, phosphate was raised from 0.18 mM to the standard 0.8 mM. The dilution rate was held constant at 0.083 h-1. For time-series array data, cultures before perturbation were allowed to reach steady state. We rapidly changed concentration(s) of H2 and/or a nutrient, and sampled at intervals after the perturbation; right away, after 5 mins, 10, 20, 30, 45, 60, 90, 120, 180, and 300 mins. Culture samples (1.5 mL) were rapidly removed from the chemostat vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.

first: Thomas

middle: J

last: Lie

first: Kyle

middle: C

last: Costa


title: Time series of Methanococcus maripaludis MM901:del_fruA (MMP1382)-del_frcA (MMP0820), a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009).   Growth conditions were carefully designed to separate the effects of different environmental factors. To ensure physico-chemical factors being constant, all cell cultures were performed using continuous cultivations with a constant dilution rate. The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). For shifts from a H2 excess to a H2 limited condition, H2 was lowered from standard 110 mL/min to 21 mL/min and Ar was raised from standard 35 mL/min to 125 mL/min. For shifts from P-limited to P-excess conditions, phosphate was raised from 0.13 mM to the standard 0.8 mM. The dilution rate was held constant at 0.083 h-1. For time-series array data, cultures before perturbation were allowed to reach steady state. We rapidly changed concentration(s) of H2 and/or a nutrient, and sampled at intervals after the perturbation; right away, after 5 mins, 10, 20, 30, 45, 60, 90, 120, 180, and 300 mins. Culture samples (1.5 mL) were rapidly removed from the chemostat vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.


title: Time series of Methanococcus maripaludis MM901, a shift from a H2-excess and N-limiting condition to a H2-limited and N-excess condition in chemostats (growth rate held constant)

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009).   Growth conditions were carefully designed to separate the effects of different environmental factors. To ensure physico-chemical factors being constant, all cell cultures were performed using continuous cultivations with a constant dilution rate. The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). For shifts from a H2 excess to a H2 limited condition, H2 was lowered from standard 110 mL/min to 21 mL/min and Ar was raised from standard 35 mL/min to 125 mL/min. Shifts from N-limited to N-excess conditions were achieved by raising NH4Cl from 2.8 mM to the standard 10 mM. The dilution rate was held constant at 0.083 h-1. For time-series array data, cultures before perturbation were allowed to reach steady state. We rapidly changed concentration(s) of H2 and/or a nutrient, and sampled at intervals after the perturbation; right away, after 5 mins, 10, 20, 30, 45, 60, 90, 120, 180, and 300 mins. Culture samples (1.5 mL) were rapidly removed from the chemostat vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.


title: Mapping the inter- and intra-chromosomal interactions of specific insulator binding sites with circular chromosome conformation capture (4C) assay (Gondor et al., 2008 Nature Protocol) [NimbleGen Array data]

status: Public on Sep 15 2013

first: Chin-Tong

last: Ong

department: Developmental Biology

institute: Temasek Life Sciences Lab

summary:
Drosophila Insulator proteins mediate long-range chromosomal interactions. ChIP-seq revealed that binding of insulator proteins to some specific DNA sites was regulated by poly(ADP-ribosyl)ation in S2 cells.
Three insulator sites regulated by poly(ADP-ribosyl)ation were used as baits to map their distant interacting sites using 4C assay in control S2 cells.

overall_design: Mapping the chromosomal interactions of three specific insulator binding sites with 4C assay in control S2 cells.

first: Victor

last: Corces


title: Expression data from Human Umbilical Vein Endothelial Cells (HUVECs) exposed to WT and V30M transthyretin (TTR)

status: Public on Sep 13 2013

city: Lisbon

first: Raquel

middle: João

last: Nunes

address: Avenida Prof Egas Moniz

department: Angiogenesis Unit

country: Portugal

institute: Instituto Medicina Molecular

summary:
The biological effects of TTR proteins in the vasculature remain unknown.
We used microarrays to detail the modulation of gene expression on HUVECs by V30M TTR when compared to cells exposed to WT TTR.

overall_design: HUVECs (passage 7) were cultured in the presence of WT or V30M TTR at 4µM for 3 hours. RNA was extracted and hybridized on Affymetrix microarrays. We sought to obtain differentially expressed genes modulated by V30M TTR protein.

first: Susana

last: Santos


title: Time series of Methanococcus maripaludis MM901:del_MMP1447, a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009). Growth conditions were carefully designed to separate the effects of different environmental factors. To ensure physico-chemical factors being constant, all cell cultures were performed using continuous cultivations with a constant dilution rate. The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). For shifts from a H2 excess to a H2 limited condition, H2 was lowered from standard 110 mL/min to 21 mL/min and Ar was raised from standard 35 mL/min to 125 mL/min. For shifts from P-limited to P-excess conditions, phosphate was raised from 0.18 mM to the standard 0.8 mM. The dilution rate was held constant at 0.083 h-1. For time-series array data, cultures before perturbation were allowed to reach steady state. We rapidly changed concentration(s) of H2 and/or a nutrient, and sampled at intervals after the perturbation; right away, after 5 mins, 10, 20, 30, 45, 60, 90, 120, 180, and 300 mins. Culture samples (1.5 mL) were rapidly removed from the chemostat vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C. Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.


title: Steady-state samples of Methanococcus maripaludis MM901 grown on formate-excess medium

summary: Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. maripaludis through integrated analysis of the transcriptome structure and a newly constructed Peptide Atlas. The environment and gene-regulatory influence network (EGRIN) model of the strain was constructed from a compendium of transcriptome data that was collected over 100 different steady-state and time course experiments that were performed in chemostats, or batch cultures, under a spectrum of environmental perturbations that modulated methanogenesis. We discovered that at least five regulatory mechanisms act in a combinatorial scheme to inter-coordinate key steps of methanogenesis with different processes such as motility, ATP biosynthesis, and carbon assimilation. Through a combination of genetic and environmental perturbation experiments we have validated the EGRIN-predicted role of two novel TFs in the regulation of phosphate-dependent repression of formate dehydorgenase -- a key enzyme in the methanogenesis pathway.

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009). The medium contained 380 mM sodium formate. The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). Hydrogen limited condition was 21 mL/min H2. Culture samples (1.5 mL) were rapidly removed from the vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.


title: Community composition of bacteria involved in fixed nitrogen loss in the water column of two major oxygen minimum zones in the ocean

status: Public on Sep 12 2013

city: Princeton

first: Xuefeng

last: Peng

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

summary: The community composition (in terms of abundance, distribution and contribution of diverse clades) of bacteria involved in nitrogen transformations in the oxygen minimum zones may be related to the rates of fixed N loss in these systems. The abundance of both denirifying and anammox bacteria, and the assemblage composition of denitrifying bacteria were investigated in the Eastern Tropical South Pacific and the Arabian Sea using assays based on molecular markers for the two groups of bacteria. The abundance and distribution of bacteria associated with the fixed N removal processes denitrification and anammox were investigated using quantitative PCR for genes encoding nitrite reductase (nirK and nirS) in denitrifying bacteria and hydrazine oxidase(hzo) and 16S rRNA genesin anammox bacteria. All of these genes had depth distributions with maxima associated with the secondary nitrite maximum in low oxygen waters. NirS was mch more abundant than nirK, and much more abundant than the 16S rRNA gene from anammox bacteria. The ratio of hzo:16S rRNA for anammox was low and variable implying greater unexplored diversity in the the hzo gene. Assemblage composition of the abundant nirS-type denitrifiers was evaluated using a funcitonal gene microarray. Of the nirS archetypes represented on the microarray, very few occurred speficically in one region or depth interval, but the assemblages varied significantly. Community composition of denitrifiers based on microarray analysis of the nirS gene was most different between geographical regions. Within each region, the surface layer and OMZ assemblages clustered distinctly. Thus, in addition to spatial and temporal variation in denitrificaiton and anammox rates, both microbial abundance and community composition also vary between OMZ regions and depths.

sample_organism:
synthetic construct
marine metagenome

overall_design: Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype).  Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array.  Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

first: A

last: Jayakumar

first: X

first: B

last: Ward


title: Time series of Methanococcus maripaludis MM901:del_MMP0719, a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)


title: Rapidly cleaving bovine embryos have a better developmental potential and a distinctive mRNA pattern

status: Public on Sep 14 2013

city: Quebec

first: Ernesto

last: Orozco-Lucero

state: Quebec

address: 2440, Boul. Hochelaga

department: Animal Science

institute: Laval University

summary: Transcriptome analysis of in vitro-produced bovine 2-cell embryos according to their time to the first cleavage. Three time points were established in order to collect all the 2-cell embryos present at each moment to contrast only the two exteme embryo subpopulations: fast against slow.

overall_design: 4 biological replicates of fast (29.5 hpf) vs. slow (46 hpf) 2-cell embryos were contrasted. Each replicate was subjected to a dye-swap procedure.

first: Isabelle

last: Dufort

first: Claude

last: Robert

first: Marc-Andre

last: Sirard


title: Chromosome conformation capture-on-chip analysis of long-range cis interactions of the SOX9 promoter

status: Public on Sep 08 2013

first: Pawel

last: Stankiewicz

address: One Baylor Plaza

department: Molecular Human Genetics

summary:
Transcription factor SOX9 is essential for the differentiation of chondrocytes and the development of testes. Heterozygous point mutations and genomic deletions involving SOX9 lead to campomelic dysplasia (CD) often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.3 Mb up- and downstream to SOX9, and likely disrupting its distant cis-regulatory elements, have been described in patients with milder forms of CD.
Performing chromosome conformation capture-on-chip (4C) analysis in Sertoli cells and lymphoblasts we identified several novel potentially cis-interacting regions both up- and downstream to SOX9, with some of them overlapping lncRNA genes preferentially expressed in testes.

overall_design: Custom designed 3x720K tiling microarrays covering 4 Mb region (chr17:68,117,161-72,122,560) flanking SOX9 gene of interest

first: Marta

last: Smyk

first: Przemyslaw

last: Szafranski

first: Michał

last: Startek

first: Anna

last: Gambin

first: Paweł


title: The Condition-Dependent Transcriptional Landscape of Burkholderia pseudomallei

first: Wen Fong

last: Ooi

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

institute: Genome Institute of Singapore

summary: Bacterial transcriptomes are dynamic, context-specific and condition-dependent. Infection by the soil bacterium, Burkholderia pseudomallei, causes melioidosis, an often fatal infectious disease of humans and animals. Possessing a large multi-chromosomal genome, B. pseudomallei is able to persist and survive in a multitude of environments. To obtain a comprehensive overview of B. pseudomallei expressed transcripts, we initiated whole-genome transcriptome profiling covering a broad spectrum of conditions and exposures – a so-called “condition compendium”. Using the compendium, we confirmed many previously-annotated genes and operons, and also identified hundreds of novel transcripts including anti-sense transcripts and non-coding RNAs. By systematically examining genes exhibiting highly similar expression patterns, we ascribed putative functions to previously uncharacterized genes, and identified novel regulatory elements controlling these expression patterns. We also used the compendium to elucidate candidate virulence pathways associated with quorum-sensing and infection in mice. Our study showcases the power of a B. pseudomallei condition compendium as a valuable resource for understanding microbial physiology and the pathogenesis of melioidosis.

sample_organism:
Burkholderia pseudomallei
Burkholderia pseudomallei K96243
Burkholderia pseudomallei Bp22

overall_design: The transcriptome profiles of Bp exposed to 82 conditions were captured using a custom-designed tiling microarray and compiled into a compendium revealing novel genomic features and co-expression network.

first: Ee Ling Catherine


title: Gene expression analysis of late exponential vs. stationary phase cultures using a custom designed Pseudo-nitzschia multiseries (Ps-n) cDNA microarray

city: Cambridge

first: Katie Rose

last: Boissonneault

address: 77 Massachusetts Ave., 76-553

department: Biology

web_link: http://to be added

institute: Massachusetts Institute of Technology

summary: Pseudo-nitzschia multiseries (Ps-n) is a toxigenic marine diatom that produces the neurotoxin, domoic acid. We screened for candidate genes that may be involved in domoic acid production by determining changes in transcript profiles in Ps-n cultures that were in late exponential (low-domoic-acid-producing) vs. stationary (high-domoic-acid-producing) growth states. We also identified a number of candidate reference genes for future RT-qPCR studies, based on their stability in this study.

overall_design: Ps-n RNA was extracted from late exponential and stationary phase cultures. Experiments included one axenic culture, and two non-axenic cultures.  Experiments were dye-swapped to account for differences in dye labeling and detection efficiencies: a) the axenic culture experiment included 4 technical replicate arrays (i.e., 2 dye-swapped experiments = 4 total hybridizations), and b) the non-axenic culture experiments each included 6 technical replicate arrays (i.e., 3 dye-swapped experiments = 6 total hybridizations).

first: KatieRose

first: Stephen

last: Bates

first: Deborah

last: Robertson

first: Sean

last: Milton

first: Jerry

last: Pelletier

first: David

middle: E

last: Housman


title: Molecular basis of 9G4 B cell autoreactivity in human SLE

status: Public on Sep 05 2013

city: Dallas

first: yun

last: lian

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: 9G4+ IgG antibodies expand in SLE in a disease specific fashion and react with different lupus antigens including B cell antigens and apoptotic cells. Their shared use of VH4-34 represents a unique system to understand the molecular basis of lupus autoreactivity. Understanding the participation of apoptotic cells, a rich source of self-antigens including chromatin, in the diversification and selection of autoreactive memory B cells is particularly important in SLE where these cells accumulate in the germinal centers and may activate pathogenic autoreactive B cells. Our findings indicate that the three mabs with  strong apoptotic binding   recognized chromatin and individual histones as documented by glomerular proteome microarrays. While the actual antigens mediating APCB remain to be formally elucidating, our initial studies indicate that binding to histone/chromatin may mediate such autoreactivity in at least a fraction of these antibodies

overall_design: Single VH4-34 B cells sorted from IgD-CD27+ memory B cells of SLE patient are sorted and single -RT-PCR is performed to generate monoclonal antibody. 3 monoclonals which were strong apoptotic binders tested for protein array against Chromatin, Histone1, Histone 2A, Histone 2B, Histone 3, Histone 4 and total histones

first: Quan-Zhen

last: Li

first: Chandra

last: Mohan

first: Ignacio

last: Sanz

first: Asiya

last: Chida

first: Christopher

last: Richardson