title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabD_WB]

status: Public on Jan 26 2015

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

country: USA

institute: Southern California Coastal Water Research Project

summary: Additional toxicity testing and regulation are needed as the number of compounds chronically released into aquatic coastal environments increases. Decision makers require comprehensive and efficient screening tools to detect adverse biological effects and to identify their cause. Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, identifying sub-lethal organismal responses and identifying contaminant classes underlying observed toxicity. Before transcriptomic information is used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps that impact the reliable identification of differentially expressed genes. A custom 15K-probe microarray was used to conduct transcriptomics analyses across six laboratories. Estuarine amphipods were exposed to cyfluthrin-spiked or control sediments for 10 days. Two sample types were generated: the first consisted of total RNA extracts (Ex) from exposed and control samples (extracted by one laboratory) and the second type consisted of exposed and control whole body amphipods (WB) from which RNA was extracted by each laboratory. A subset of genes were consistently identified as differentially expressed across all laboratories and sample types. Genes with the highest magnitude of differential expression (> 2 fold) were more likely to be consistently identified as differentially expressed across laboratories. Differentially expressed data had a higher degree of concordance across all laboratories (W = 0.7) in samples with similar RNA quality (Ex) when compared to WB samples (W = 0.5). Our results revealed that several factors can affect data comparability including RNA sample preparation, labeling, instrumentation and technical expertise.

overall_design:
First dataset: RNA extracts (Ex) derived from whole bodies of 8 controls and 8 cyfluthrin-exposed amphipods were prepared by one single lab and analyzed (i.e., labeling, microarray hybridization and feature extraction) by all 6 laboratories.
Second dataset: Each of the 6 labs received 8 control and 8 cyfluthrin-exposed whole body samples (WB) for RNA extraction and microarrays. Lab C was unable to analyze the WB samples and only submitted data for the Ex samples.

first: Doris

last: Vidal-Dorsch

first: Steven

last: Bay

first: Shelly

last: Moore

first: Blythe

last: Layton

first: Chris

last: Vulpe

first: Marianna

last: Brown-Augustine

first: Alex

last: Loguinov

first: Helen

last: Poynton

first: Natalia

last: Garcia-Reyero

first: Edward

last: Perkins

first: Lynn

last: Escalon

first: Nancy

last: Denslow

first: Cristina

last: Colli-Dula

first: Tri

last: Doan

first: Shweta

last: Shukradas

first: Joy

last: Bruno

first: Lorraine

last: Brown

first: Graham

last: Van Agglen

first: Paula

last: Jackman

first: Megan

last: Bauer


title: High-resolution genome-wide transcriptomics analysis of O. dioica during recovery from growth arrest

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

type: Expression profiling by genome tiling array

summary: Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in the marine chordate Oikopleura dioica and find evidence for proposed functions of SL-trans-splicing. A recent hypothesis postulates that operons facilitate recovery from growth arrested states in metazoans. We examined the expression dynamics of operons across the life-cycle of the animal and during growth arrest recovery. We show that operons do not facilitate recovery from growth arrest in O. dioica. We find that operons are enriched in the germline and that trans-spliced transcripts are predominantly maternal., Interestingly, there is a TOP-like motif in the SL sequence, and trans-splicing in TOP mRNAs, indicating that trans-spliced mRNAs are targets for nutrient-dependent translational control in O. dioica.

overall_design: Whole animals were sampled from a growth arrested state as well as three time points after release from growth arrest: 0.5 hrs; 1.5 hrs and 4 hrs.  Two biological replicates were performed for each time point and each of these was divided into three technical replicates.

first: Gemma

middle: B

last: Danks

first: Martina

last: Raasholm

first: Coen

last: Campsteijn

first: Abby

middle: M

last: Long

first: J

middle: R

last: Manak

first: Boris

last: Lenhard


title: In embryo analysis of H3K27 trimethylation suggests a two-step process involving PRC2 interacting sequences and high GC content

status: Public on Jan 27 2015

city: Lausanne

first: Patrick

last: Schorderet

state: Vaud

address: SV 2842 (Bâtiment SV)  Station 19

department: ISREC

country: Switzerland

institute: EPFL

type: Genome binding/occupancy profiling by genome tiling array

summary: ABSTRACT  Polycomb group (PcG) proteins are essential for the repression of key developmental regulators during development. In Drosophila, the polycomb repressive complexes (PRC) associate with defined DNA sequences termed polycomb response elements (PREs). In mammals, however, the mechanisms underlying polycomb recruitment at targeted loci are poorly understood. We have used an in vivo approach to try and map DNA sequences of importance for the proper recruitment of polycomb proteins within the genetically well-characterized HoxD genomic locus. Here, we report that relatively small polycomb interacting sequences appear necessary and sufficient to confer polycomb recognition and targeting to ectopic loci. These elements synergize, when clustered together, to form a fully functional repressive domain. In addition, a high GC content, while not sufficient to recruit PRC2, may help its local spreading. We discuss the importance of PRC2 recruitment over Hox gene clusters, in embryonic stem cells, for their subsequent coordinated transcriptional activation during development.

overall_design: ChIP-chip using K27 antibodies

first: Nicolas

last: Lonfat

first: Fabrice

last: Darbellay

last: Tschopp

first: Sandra

last: Oesch

first: Natalia

last: Soshnikova

first: Denis

last: Duboule


title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabC_Ex]

first: Alvine

last: Mehinto

first: Doris

last: Vidal-Dorsch

first: Steven

last: Bay

first: Shelly

last: Moore

first: Blythe

last: Layton

first: Chris

last: Vulpe

first: Marianna

last: Brown-Augustine

first: Alex

last: Loguinov

first: Helen

last: Poynton

last: Garcia-Reyero

first: Edward

last: Perkins

first: Lynn

last: Escalon

first: Nancy

last: Denslow

first: Cristina

last: Colli-Dula

first: Tri

last: Doan

first: Shweta

last: Shukradas

first: Joy

last: Bruno

first: Lorraine

last: Brown

last: Van Agglen


title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabA_WB]

first: Alvine

last: Mehinto

last: Vidal-Dorsch

last: Bay

first: Natalia

first: Graham

first: Paula

last: Jackman

first: Megan

last: Bauer


title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabA_Ex]

first: Doris

first: Steven

first: Shelly

last: Moore

first: Blythe

last: Layton

first: Chris

last: Vulpe

last: Brown-Augustine

last: Loguinov


title: Disruption of transkingdom communication by antibiotics leads to immune and mitochondrial dysfunction in the gut (LMD)

city: Corvallis

last: Shulzhenko

state: Oregon

address: 700 SW 30th St, 105 Dryden Hall

institute: Oregon State University

summary:
We analyzed the effects of antibiotics using a popular model of gut microbiota depletion in mice by a cocktail of antibiotics. We combined intestinal transcriptome together with metagenomic analysis of the gut microbiota to develop a new bioinformatics approach that probes the links between microbial components and host functions. We found that most antibiotic-induced alterations can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues; and the effects of remaining antibiotic-resistant microbes. While microbe depletion led to down-regulation of immunity, the two other factors primarily inhibited mitochondrial gene expression and amounts of active mitochondria, and induced cell death. By reconstructing and analyzing a transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria.
This series includes gene expression of the laser microdissected compartments of the ileum such as villous epithelium, lamina propria and crypts from specific pathogen free mice

overall_design: common reference design with a pool of small intestine RNA labeled with Cy3

first: Andrey

last: Morgun


title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabD_Ex]

first: Marianna

first: Alex

first: Helen

last: Poynton

last: Garcia-Reyero

first: Edward

last: Perkins

first: Lynn

last: Escalon

first: Nancy

last: Denslow

last: Colli-Dula

last: Doan


title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabE_Ex]

first: Alvine

last: Mehinto

last: Vidal-Dorsch

last: Bay

first: Cristina

first: Tri

first: Shweta

last: Shukradas

first: Joy

last: Bruno

first: Lorraine

last: Brown

last: Van Agglen


title: Integrative genomic and transcriptomic characterization of matched primary and metastatic liver and colorectal carcinoma

status: Public on Jan 22 2015

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

type: Genome variation profiling by genome tiling array

summary: Somatic copy number alterations of 17 paired tumor and metastasis tissue samples were measured by Agilent array-based comparative genomic hybridization (CGH).  Seven colon adenocarcinomas with paired liver metastasis and 10 liver carcinoma with metastasis to the lymph node, adrenal gland or lung were analyzed.

first: Stephanie

last: Roessler

middle: W


title: Acute heat stress induces differential gene expressions in the testes of a broiler-type strain of Taiwan country chickens

city: Taichung

first: San

middle: Yuan

last: Huang

address: Kuo-Kuang Rd.

department: Animal science

country: Taiwan

institute: National Chung Hsing University

summary: To realize the gene expression in response to acute heat stress in chicken testis, we have employed whole genome microarray expression profiling as we have employed whole genome microarray expression profiling as a tool to identify genes response to acute heat stress. Male B strain Taiwan country chickens were subjected to acute heat stress (38℃) for 4 h, and then exposed to 25℃, with testes collected 0, 2, and 6 h after the cessation of heat stress, using non heat-stressed roosters as a control group (n = 3 roosters per group). Based on a chicken 44K oligo microarray, 163 genes significantly differed in the testes of the heat-stressed chickens from those of the control chickens. The mRNA expressions of upregulated genes, including HSP25, HSP90AA1, HSPA2, and LPAR2, and downregulated genes, including CDH5, CTNNA3, EHF, CIRBP, SLA, and NTF3, were confirmed through quantitative real-time polymerase chain reaction (qRT-PCR).

overall_design: Acute heat stress induced testicular gene experssion in B strain Taiwan country chicken was measured at 0, 2, and 6 h of recovery after 4 h of 38 degree acute heat stress.

first: San-Yuan

first: Shih-Han

first: Chuen-Yu

last: Cheng

first: Pin-Chi

last: Tang

first: Chih-Feng

last: Chen

first: Hsin-Hsin

first: Yen-Pai

last: Lee


title: Bacillus subtilis WalR (YycF) ChIP-chip  Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Identification of the specific WalR (YycF) binding regions on the B. subtilis chromosome during exponential and phosphate starvation growth phases. The data serves to extend the WalRK regulon in Bacillus subtilis and its role in cell wall metabolism, as well as implying a role in several other cellular processes.

overall_design: For each sample analyzed in this study three biological replicates were performed. Three different samples were taken from a strain expressing the WalR-SPA protein as well as from wild-type (168) without a tagged WalR. Samples were taken from exponentially growing cells in low phosphate medium (LPDM) as well as from phosphate-limited cells (T2). Each sample compares ChIP DNA vs. Total DNA from the same cells.

first: Letal

middle: I

last: Salzberg

first: Kevin

last: Devine


title: Organic matter loading modifies the microbial community responsible for nitrogen loss in estuarine sediments

status: Public on Jan 30 2015

city: Princeton

first: Bess

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

summary: Coastal marine sediments, as locations of substantial fixed nitrogen loss, are very important to the nitrogen budget and to the primary productivity of the oceans. Coastal sediment systems are also highly dynamic and subject to periodic natural and anthropogenic organic substrate additions. The response to organic matter by the microbial community involved in nitrogen loss processes was evaluated using mesocosms of Chesapeake Bay sediments. Over the course of a 50-day incubation, rates of anammox and denitrification were measured weekly using 15N tracer incubations, and samples were collected for genetic analysis. Rates of both nitrogen loss processes and gene abundances associated with them corresponded loosely, probably because heterogeneities in sediments obscured a clear relationship. The rates of denitrification were stimulated more by the higher organic matter addition, and the fraction of nitrogen loss attributed to anammox slightly reduced. Furthermore, the large organic matter pulse drove a significant and rapid shift in the denitrifier community as determined using a nirS microarray, indicating the diversity of these organisms plays an essential role in responding to anthropogenic inputs. We also suggest that the proportion of nitrogen loss due to anammox in these coastal estuarine sediments may be underestimated due to temporal dynamics as well as from methodological artifacts related to conventional sediment slurry incubation approaches.

sample_organism:
synthetic construct
aquatic 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: Andrew

last: Babbin

first: Amal

last: Jayakumar


title: Microarray analysis among non-alcoholic fatty liver, non-alcoholic steatohepatitis, and type 2 diabetes mellitus rats

status: Public on Jan 23 2015

city: Shanghai

first: Xiaolin

last: Liu

address: Chongqingnan road, 280

country: China

institute: School of Medicine, Shanghai Jiao Tong University

summary:
Non-alcoholic fatty liver (NAFL) has the potential to progress to non-alcoholic steatohepatitis (NASH) or to promote type 2 diabetes mellitus (T2DM). However, NASH and T2DM do not always develop coordinately. We established rat models of NAFL, NASH, and NAFL + T2DM to recapitulate different phenotypes associated with NAFLD and its progression. Microarrays were used to identify hepatic gene expression changes in each of these models. The goal is to identify a predictor of different NAFLD progressions.
Non-alcoholic fatty liver disease (NAFLD) is recognized as a low-grade systemic inflammatory state with both hepatic and extra-hepatic manifestations. We aimed to identify common key regulators and adaptive pathways in different NAFLD phenotypes. NAFL, NASH and NAFL+T2DM rat models were used to represent simple fatty liver, fatty liver with severe hepatic manifestations, and fatty liver with severe metabolic manifestations, respectively. We applied microarray analysis to characterize the key regulators and adaptive pathways in different NAFLD phenotypes.

overall_design: There are 12 samples in our study which belonged to 4 groups, and each group contains 3 different samples.

first: Yanan

last: Ming

first: Jingyi

last: Zhang

first: Yimin

last: Mao


title: PACT-PKR Pathway Transactivates the Tumor Suppressor RhoB through C/EBPbeta in Cancer Cells with High Akt Activity

status: Public on Jan 29 2015

first: Phillip

middle: A

last: Dennis

address: 37 Convent Dr.

department: MOB, CCR

institute: NCI

summary: Activation of the PI3K/Akt/mTOR pathway in cancers can occur through loss of PTEN. Transcriptional profiling of pathway inhibitors identified the tumor suppressor RhoB as a gene markedly upregulated by lipid-based Akt inhibitors (LBAI). Here, we demonstrate that the C/EBPbeta full-length isoform LAP is responsible for transcriptional induction through its binding site within the RhoB proximal promoter. LBAI strongly transactivate RhoB by switching translation of C/EBPbeta from the truncated isoform LIP to LAP via PACT-mediated PKR activation in cancer cells with high Akt activity. Unlike PTEN commonly mutated, endogenous RhoB tumor-suppressive activity can be reconstituted by restoring its expression, which was noninvasively monitored by a RhoB promoter-driven luciferase reporter in living mice. LBAI administration increased luciferase activity and decreased the growth of human tumor xenografts. Increased PKR activation by LBAI leads to more robust RhoB induction and cytotoxicity than other PI3K/Akt/mTOR axis inhibitors, revealing a novel strategy for cancer therapy.

overall_design: H157 cells were plated 2 x 10^6 in T-75 flasks in RPMI 1640 containing 10% FBS and incubated for 24h. The medium was then changed to RPMI 1640 with 0.1% FBS and the cells were incubated overnight. The following morning, cells were treated with 10 microM of LY294002, OSU03012, PIA23, Perifosine, Miltefosine, API-2, DZ-50, or 100 nM of Wortmannin and Rapamycin for 6 hours, or an equal amount of DMSO as control. Following incubation, total RNA was extracted from cells in T-75 flasks using TRIzol reagent (Invitrogen). Two dye-swapped replicates were performed for each treatment.

first: Chunyu

first: Abdel

middle: G

last: Elkahloun


title: Drug screening and genomic analyses of HER2 positive breast cancer cell lines reveal predictors for treatment response [Expression profiling]

city: Oslo

first: Sandra

last: Jernström

address: Ullernchausséen 70

department: Genetics

institute: OUS The Norwegian Radium hospital

summary: Thirteen HER2 positive breast cancer cell lines were screened with 22 commercially available compounds, mainly targeting proteins in the ErbB2 signaling pathway, and the molecular mechanisms related to treatment response were sought. To search for response predictors, genomic and transcriptomic profiling, PIK3CA mutations and PTEN status were associated to the drug responses and several genes involved in the response of the compounds were identified.

overall_design: RNA from thirteen HER2 positive breast cancer cell lines was isolated and hybridized on Affymetrix arrays.

first: Vesa

last: Hongisto

first: Suvi-Katri

last: Leivonen

first: Eldri

middle: U

last: Due

first: Dagim

middle: S

last: Tadele

first: Henrik

last: Edgren

first: Olli

last: Kallioniemi

first: Merja

last: Perälä

first: Anne-Lise

last: Børresen-Dale

first: Gunhild

last: Mælandsmo

first: Kristine

middle: K

last: Sahlberg


title: Drug screening and genomic analyses of HER2 positive breast cancer cell lines reveal predictors for treatment response [CGH]

summary:
Thirteen HER2 positive breast cancer cell lines were screened with 22 commercially available compounds, mainly targeting proteins in the ErbB2 signaling pathway, and the molecular mechanisms related to treatment response were sought. To search for response predictors, genomic and transcriptomic profiling, PIK3CA mutations and PTEN status were associated to the drug responses and several genes involved in the response of the compounds were identified.
Array-CGH experiments of HER2+ breast cancer cell lines grown under standard conditions.

overall_design: DNA from four HER2 positive breast cancer cell lines was isolated and hybridized on Agilent arrays.


title: Disruption of transkingdom communication by antibiotics leads to immune and mitochondrial dysfunction in the gut (main)

first: Natalia

last: Shulzhenko

summary:
We analyzed the effects of antibiotics using a popular model of gut microbiota depletion in mice by a cocktail of antibiotics. We combined intestinal transcriptome together with metagenomic analysis of the gut microbiota to develop a new bioinformatics approach that probes the links between microbial components and host functions. We found that most antibiotic-induced alterations can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues; and the effects of remaining antibiotic-resistant microbes. While microbe depletion led to down-regulation of immunity, the two other factors primarily inhibited mitochondrial gene expression and amounts of active mitochondria, and induced cell death. By reconstructing and analyzing a transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria.
This series includes gene expression in the ileum of control, antibiotics (ABx)-treated, germfree, germfree-ABx-treated and mice colonized with normal or Abx-resistant microbiota.

first: Andrey

last: Morgun


title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabE_WB]

first: Alvine

last: Mehinto

first: Doris

last: Vidal-Dorsch

first: Steven

last: Bay

first: Shelly

last: Moore

first: Blythe

last: Layton

first: Chris

last: Vulpe

first: Marianna

last: Brown-Augustine

first: Alex

last: Loguinov

first: Helen

last: Poynton

last: Garcia-Reyero

first: Edward

last: Perkins

first: Lynn

last: Escalon

first: Nancy

last: Denslow

first: Cristina

last: Colli-Dula

first: Tri

last: Doan

first: Shweta

last: Shukradas

first: Joy

last: Bruno

first: Lorraine

last: Brown

first: Graham

last: Van Agglen

first: Paula

last: Jackman

first: Megan

last: Bauer


title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabB_Ex]

first: Alvine

last: Mehinto

first: Doris

last: Vidal-Dorsch

first: Steven

last: Bay

first: Shelly

last: Moore

last: Layton

first: Natalia


title: Drug screening and genomic analyses of HER2 positive breast cancer cell lines reveal predictors for treatment response

first: Sandra

last: Jernström

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

overall_design: Refer to individual Series


title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabF_WB]

first: Blythe

first: Chris

last: Vulpe

first: Marianna

last: Brown-Augustine

first: Alex

last: Loguinov

first: Helen

last: Poynton

last: Garcia-Reyero

first: Edward

last: Perkins


title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabB_WB]

first: Lynn

last: Escalon

first: Nancy

last: Denslow

first: Cristina

last: Colli-Dula

first: Tri

last: Doan

first: Shweta

last: Shukradas

first: Joy

last: Bruno


title: Expression data from bovine oocyte; Identification of molecular markers for oocyte competence in bovine cummulus cells

city: Sao Paulo

first: Renata

last: Pellegrino

address: Rua NApoleao de Barros 925

country: Brazil

institute: UNIFESP

summary:
Despite great improvements in assisted reproductive technology (ARTs), the success of in vitro embryo production remains relatively low. Most of the oocytes used to produce in vitro embryos are recovered from smaller follicles, forming a heterogeneous population that must be matured in vitro. Since the original in vitro maturation (IVM ) experiments (Heilbrunn et al. , 1939) the process by which the most competent oocytes are selected to produce blastocysts remains similar and is still based on morphological aspects of the oocyte cytoplasm and the number of layers and compaction of cumulus cells attached to the oocyte surface (Armstrong, 2001, Coticchio et al. , 2004, Krisher, 2003, Lonergan et al. , 2003).
Ovaries from crossbred cows (Bos indicus x Bos taurus) were collected immediately after slaughter and transported to the laboratory in saline solution (0.9% NaCl) supplemented with penicillin G (100 IU/mL) and streptomycin sulfate (100 mg/mL) at 35-37C. The follicles were dissected from the ovarian cortex using scissors, scalpels and tweezers in TCM-199 medium supplemented with Hank’s salts and 10% fetal calf serum (FCS; GIBCO BRL) at 36C. Follicles were measured using a graduated eyepiece (OSM-4; Olympus) and then classified morphologically into two groups according to their diameter: 1.0-3.0 mm or ≥8.0 mm. The criteria used for follicle selection included the presence of extensive and fine vascularization and a shiny and translucent appearance. After follicular rupture, the presence of granulosa cells with a regular and healthy appearance and no free-floating particles in the follicular fluid were also used as selection criteria. Only COCs with a homogeneous granulated cytoplasm and at least three layers of compact of cumulus cells were used in the present study. The selected COCs were transferred to a 50 μL droplet of phosphate-buffered saline (PBS), and the cumulus cells were mechanically removed by repeated pipetting. After cumulus collection, they were transferred to a 0.2-mL tube and centrifuged twice for 2 min at 700 g. The supernatant was removed, and 2μL of RNAlater (Applied Biosystems, Foster City, CA, USA) was added to the pellet, which was then stored at -20C until RNA extraction. For each follicle size group, three replicas of pooled cumulus cells corresponding to 30 oocytes were stored for RNA extraction and subsequent microarray assays, and four independent replicates corresponding to 20 oocytes were stored for RNA extraction for subsequent qPCR assays.

overall_design: During oogenesis, the somatic cells that surround the oocyte proliferate and differentiate into cumulus cells (CCs), which are metabolically coupled to the oocyte, forming the cumulus-oocyte complexes (COCs) (van den Hurk and Zhao, 2005). The CCs remain in strong contact with the oocyte, maintained by cytoplasmic bridges called gap-junctions, as well as through justacrine and paracrine signaling networks (Albertini et al. , 2001, Gilchrist et al. , 2004, Tanghe et al. , 2002, Vozzi et al. , 2001, Webb et al. , 2002). This intense bidirectional communication between the CCs and the oocyte is maintained during all phases of folliculogenesis and is essential for the acquisition of oocyte competence that is required for blastocyst development (Assidi et al., 2008, Fair, 2003, Gilchrist et al., 2004). An informative model to access the level of oocyte competence that has been used by many research groups is follicle size (Donnison and Pfeffer, 2004, Franco et al. , 2013, Lequarre et al. , 2005, Mourot et al., 2006). In a previous study, we showed that oocytes obtained from follicles 1-3 mm in diameter are significantly less competent in producing blastocysts than oocytes obtained from follicles ≥8 mm in diameter (Franco et al., 2013). In the present study, we use the same model to compare the gene expression profile of more than 23,000 bovine transcripts between the CCs obtained from incompetent COCs (1-3 mm) and competent COCs  (≥8 mm). We have found substantial differences in the expression of several gene clusters representing distinct metabolic pathways such as energy metabolism, cell signaling, cell cycle, DNA repair, meiosis, and inflammation.

first: E

middle: O

last: Melo

first: M

last: Dode


title: Ecotoxicogenomics: interlaboratory comparability of microarray data

first: Alvine

last: Mehinto


title: Disinfectant-resistant Listeria monocytogenes strains indentified in a Iberian pork plant: S1 [160908] vs S10_1 [160908]

status: Public on Jan 24 2015

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

summary: Transcriptional profiling of two disinfectant-resistant Listeria monocytogenes strains indentified in a Iberian pork plant, S1 [160908] vs S10_1 [160908], in presence of 1.25 mg/L of Benzalkonium chloride

overall_design: One condition experiment, S1 [160908] vs. S10_1 [160908] strains. Biological replicates: 3 replicates of S1 [160908], 3 replicates of S10 [160908].

first: Sagrario

last: Ortíz

first: Joaquín

middle: V

last: Martínez-Suarez


city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Expression and differential expression analysis of breast cancer patient samples and normal samples from breast reduction operations. Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study -- Oslo I from various hospitals between 1995 and 1998 (Naume et al. "Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer." Mol Oncol 2007, 1: 160-171; Wiedswang et al. "Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer." J Clin Oncol 2003, 21: 3469-3478.). Breast tissue samples from breast reduction operations were provided from the Colosseum Clinic, Oslo in co-operation with Akershus University Hospital, Lørenskog and are referred to as normal tissue. Expression and differential expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004).  In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850.

overall_design: We analyzed 5 to 6 arrays each for breast cancer patient samples and normal samples.

first: Katharina

last: Kasack

first: Stephan

last: Schreiber

first: Torben

last: Lüders

first: Eldri

last: Due

first: Bjørn

last: Naume

first: Margit

last: Riis

first: Vessela

middle: N

last: Kristensen

first: Friedemann

last: Horn

first: Anne-Lise

last: Børresen-Dale

first: Jörg

last: Hackermüller

first: Lars

last: Baumbusch


title: Expression and differential expression analysis of HFF cells in G0 phase compared to cells in G1 using nONCOchip 2.0 array

summary: Expression and differential expression analysis of long non-coding RNAs and protein-coding genes. HFF cells were synchronised by serum starvation and reside in G0 phase or G1 phase of mitotic cell cycle.

overall_design: We analyzed three arrays each for HFF cells in G0 phase and cells in G1 phase

first: Kurt

last: Engeland


title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabF_Ex]

first: Alvine

last: Mehinto

summary: Additional toxicity testing and regulation are needed as the number of compounds chronically released into aquatic coastal environments increases. Decision makers require comprehensive and efficient screening tools to detect adverse biological effects and to identify their cause. Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, identifying sub-lethal organismal responses and identifying contaminant classes underlying observed toxicity. Before transcriptomic information is used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps that impact the reliable identification of differentially expressed genes. A custom 15K-probe microarray was used to conduct transcriptomics analyses across six laboratories. Estuarine amphipods were exposed to cyfluthrin-spiked or control sediments for 10 days. Two sample types were generated: the first consisted of total RNA extracts (Ex) from exposed and control samples (extracted by one laboratory) and the second type consisted of exposed and control whole body amphipods (WB) from which RNA was extracted by each laboratory. A subset of genes were consistently identified as differentially expressed across all laboratories and sample types. Genes with the highest magnitude of differential expression (> 2 fold) were more likely to be consistently identified as differentially expressed across laboratories. Differentially expressed data had a higher degree of concordance across all laboratories (W = 0.7) in samples with similar RNA quality (Ex) when compared to WB samples (W = 0.5). Our results revealed that several factors can affect data comparability including RNA sample preparation, labeling, instrumentation and technical expertise.

first: Doris

last: Vidal-Dorsch

first: Steven

last: Bay

first: Shelly

last: Moore

first: Blythe

last: Layton

first: Chris

last: Vulpe

first: Marianna

last: Brown-Augustine

first: Alex

last: Loguinov

first: Helen

last: Poynton

first: Natalia

last: Garcia-Reyero

first: Edward

last: Perkins

first: Lynn

last: Escalon

first: Nancy

last: Denslow

first: Cristina

last: Colli-Dula

first: Tri

last: Doan

first: Shweta

last: Shukradas

first: Joy

last: Bruno

first: Lorraine

last: Brown

first: Graham

last: Van Agglen

first: Paula

last: Jackman

first: Megan

last: Bauer


title: Transcript profiling of seven tissues in P. glauca

status: Public on Jan 21 2015

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

country: Canada

institute: Université Laval

summary: The goal is to identify tissue specific patterns of expression in Picea glauca seedlings

platform_organism:
Picea glauca
Picea sitchensis

overall_design: One-color comparison of seven tissues of white spruce. Four biological repetitions per tissue (non-related trees), repeated in two channels as technical replicates, for a total of 56 slides.

first: Elie

last: Raherison

first: Sébastien

last: Caron

first: Isabelle

last: Giguère


title: Candidatus pelagibacter ubique HTCC1062 requires 4-amino-5-hydroxymethyl-2-methylpyrimidine, an abundant thiamine precursor in the sea

status: Public on Jan 20 2015

first: Paul

last: Carini

address: 220 NASH hall

institute: Oregon State U

summary: Thiamine is often undetectable in ocean surface waters where Pelagibacter cells are numerically abundant.  Despite this, Pelagibacter cells are missing de novo thiamine synthesis pathways.  We show that an eogenous source of the thiamine precursor HMP is required for thiamine synthesis in Pelagibacter and that this precursor is abundant in the Sargasso sea.

platform_organism:
Candidatus Pelagibacter ubique HTCC1002
Candidatus Pelagibacter ubique HTCC1062
Candidatus Pelagibacter sp. HTCC7211

overall_design: Batch cultures of P. ubique were grown in a defined arificial seawater media. Three cultures were given no thiamine amendment, and three other cultures received an excess concentration of thiamine. Cultures were harvested for microarray analyses just prior to and after thiamine limitation for the purpose of observing differences in gene expression related to thiamine limitation.

first: Stephen

middle: J

last: Giovannoni


title: MtDASH Gain and loss of function mutants

first: Jerome

last: Verdier

address: 3888 Chenhua road

institute: PSC, CAS

summary: Comparison between transcriptomes of dash mutants vs WT plants and ectopic expression of 35S::DASH in hairy roots versus empty vector

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design:
Loss of function: 3 WT plants A17 at 8 days after pollination and 3 dash mutant plants at 8 days afer pollination. Gain of function transformants: 3 transformed plants containing empty vector and 4 transformed plants containing 35S::DASH
Total RNA was extracted using a modified cetyltrimethylammonium bromide method (Verdier et al., 2008). 5ug of total RNA from each sample was purified (RNeasy MinElute Cleanup kit; Qiagen) according to the manufacturer?s instructions. RNA was quantified and evaluated for purity using an ND-1000 Nanodrop Spectrophotometer (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent). The Affymetrix M. truncatula GeneChip Array (Affymetrix) was used for expression analysis during seed development. RNA from three (for dash mutant analysis) and four (for DASH ectopic expression analysis) independent biological replicates were analysed for each time point. Probe synthesis/labelling was carried out from 500 ng of RNA using the GeneChip 3?IVT express kit, according to the manufacturer?s instructions (Affymetrix). Array hybridization, scanning, and data normalization were performed as described by Benedito et al., (2008). Each file from the hybridized Affymetrix array was exported from GeneChip Operating Software version 1.4 (Affymetrix) and imported into Robust Multiarray Average Express (Irizarry et al., 2003) for global normalization. Presence/absence call for each probe set to remove background noise was obtained using dCHIP (Li and Wong, 2001). To identify probe sets differentially expressed in dash mutant vs WT control, the R package Anapuce (J. Aubert, UMR 518 AgroParisTech/INRA) was used. For each probe set, a paired t-test was performed on the log2 expression data from three arrays (3 independent biological repeats for 8 dap data), assuming that the variance of the log expression was the same for all transcripts per genotype. Spots with extreme specific variance, too low or too high, were excluded from the statistical analysis (details on the procedure given in Gagnot et al., 2008). P-values were adjusted by the Benjamini-Hochberg method (Benjamini and Hochberg, 1995), which controls the family-wise error rate.


title: Development of miRNA expression signatures of MEFs deficient in a ER stress mediator ATF4 for tunicamycin treatment

status: Public on Jan 18 2015

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

country: Japan

institute: Institute for Genome Research

summary: To further development of our miRNA expression approach to ER stress, we have employed miRNA microarray expression profiling as a discovery platform to identify ER stress-responsible ones.   Mouse embryonic fibroblasts (MEFs) deficient in a ER stress mediator ATF4 were treated with tunicamycin for 12 or 24 hrs. miRNAs responsible for tunicamycin-treatment for 12hrs in ATF4-dependent manner were extracted. Among them, expression of three miRNAs (miR-193b, miR-423-5p, miR-199a-3p) was quantified in the RNA samples from  the same as the microarray by real-time PCR.

overall_design: Mouse embryonic fibroblasts (MEFs) deficient in a ER stress mediator ATF4 were treated with 2ug/mL tunicamycin for 12 or 24 hrs. Two independent experiments were performed at each time (untreated, 12 or 24 hrs). miRNAs responsible for tunicamycin-treatment for 12hrs in ATF4-dependent manner were extracted.

first: Taiji

last: Ito

first: Tomoko

last: Mori

first: Robert

last: Zheng

first: Chinobu

last: Miyamoto

first: Kazue

last: Tsugawa

first: Kiyoe

last: Kurahashi

first: Mari

last: Funahashi

first: Ryosuke

last: Sato

first: Naoko

last: Miura

first: Kazuna

last: Takahara

first: Miho

first: Masato

last: Miyake


title: Development of miRNA expression signatures of MEFs deficient in a ER stress mediator ATF6b for tunicamycin treatment

summary: To further development of our miRNA expression approach to ER stress, we have employed miRNA microarray expression profiling as a discovery platform to identify ER stress-responsible ones.   Mouse embryonic fibroblasts (MEFs) deficient in a ER stress mediator ATF6b were treated with tunicamycin for 12 or 24 hrs. miRNAs responsible for tunicamycin-treatment for 12hrs in ATF6b-dependent manner were extracted. Among them, expression of three miRNAs (miR-15b, miR-20b, miR-92a) was quantified in the RNA samples from  the same as the microarray by real-time PCR.

overall_design: Mouse embryonic fibroblasts (MEFs) deficient in a ER stress mediator ATF6b were treated with 2ug/mL tunicamycin for 12 or 24 hrs. Two independent experiments were performed at each time (untreated, 12 or 24 hrs). miRNAs responsible for tunicamycin-treatment for 12hrs in ATF6b-dependent manner were extracted.


title: Transcriptome-wide analysis of active xylem in White Spruce and Norway Spruce during the growth season

first: John

last: MacKay

summary: The goal is to look at changes in the pattern of expression of the xylem transcriptome through the growth season in two spruces (Picea glauca and Picea abies).

sample_organism:
Picea abies
Picea glauca

overall_design: One-color comparison of active xylem collected in June, July, August and September, in two spruce species. Six biological repetitions per time point and specie, for a total of 48 slides.

first: Isabelle

last: Giguere

first: Sébastien

last: Caron

first: Elie

last: Raherison


title: Identification of molecules from dying cells that act as signals to promote proliferation of surrounding cells

status: Public on Jan 08 2015

city: Kyoto

first: Shunsaku

last: Nakagawa

address: Kawahara-cho

department: Department of Pharmacy

institute: Kyoto University Hospital

summary: To elucidate the mechanisms underlying epithelial homeostasis, we explored molecules that might serve as “danger” signals in mediating epithelial regeneration with microarray. We hypothesize that soluble factors may have been released from damaged cells to stimulate the proliferation of surviving epithelial cells. In elucidating the mechanism of dying cell-to-surviving cell communication using normal rat kidney NRK-52E epithelial cells, we observed gene expression profiles in these cells after the induction of cell death using hydrogen peroxide. The results demonstrated up-regulation of Interleukin-6, Heme oxygenase-1 and Hypoxia inducible factor-1 alpha in dying cells.

overall_design: Global gene expression changes were measured after induction of cell death in NRK-52E cells after incubation with hydrogen peroxide. Hydrogen peroxide (0, 0.003, 0.006, 0.009% in DMEM) was teated for 1 hour. After wash with PBS, cells were incubated with non-serum DMEM for 12 hours.


title: Xanthomonas oryzae pv. oryzicola (Indian Isolate) wild type and complented strains vs rpfF mutant grown under iron starved condition

status: Public on Jan 02 2015

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Transcriptional profiling of DSF regulon under iron starvation in Xanthomonas oryzae pv. oryzicola (Xoc; BXOR1) using wild type, rpfF mutant and rpfF mutant with complementing plasmid pSC9. Cell-cell signalling mediated by quorum sensing molecule known as Diffusible signalling factor (DSF) is required for the virulence of Xanthomonas group of plant pathogens. The transcriptional profiling in this study is to elucidate the role of DSF in iron acquisition under the iron limitting environment which would lead to successful colonization and pathogenesis inside host.

overall_design: Agilent one-color experiment, Organism: Xanthamonus oryzicola, (AMADID-041087)  Genotypic Technology Pvt. Ltd. designed Custom Xanthamonus oryzicola  8x15k Gene expresssion Array, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Subhadeep

last: Chatterjee

first: Rikky

last: Rai


title: Transcriptome analysis of lungs from six different mouse strains after infection with highly pathogenic H5N1 influenza A virus

status: Public on Jan 09 2015

city: St Louis

first: Adrianus

middle: Cornelis Maria

last: Boon

state: Missouri

address: 660 Euclid Avenue

department: Department of Medicine

institute: Washington University School of Medicine


title: DNA methylation profiles of human prefrontal cortex

city: Baltimore

first: Jerry

last: Guintivano

address: 720 Rutland Avenue, Ross 1068

institute: Johns Hopkins University

type: Methylation profiling by genome tiling array

summary: Using post mortem prefrontal cortex material provided by the Harvard Brain Tissue Resource Center at McLean Hospital, DNA methylation data was generated using CHARM.

overall_design: Genomic DNA was isolated and hybridized to custom-designed Nimblegen microarrays (CHARM human array v1) (n=22)

first: Zachary

last: Kaminsky

first: Ilenna

last: Jones

first: Ranjana

last: Verma

first: Lena

last: Saleh

first: Hersh

last: Trivedi

first: Richard

last: Lee

first: James

middle: B

last: Potash


title: p53 prevents neurodegeneration by regulating synaptic genes

status: Public on Jan 06 2015

city: Boston

first: Peter

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: DNA damage has been implicated in neurodegenerative disorders, including Alzheimer’s disease and other tauopathies, but the consequences of genotoxic stress to postmitotic neurons are poorly understood. Here we demonstrate that p53, a key mediator of the DNA damage response, plays a neuroprotective role in a Drosophila model of tauopathy. Further, through a whole-genome ChIP-chip analysis we identify genes controlled by p53 in postmitotic neurons. We genetically validate a specific pathway, synaptic function, in p53-mediated neuroprotection. We then demonstrate that the control of synaptic genes by p53 is conserved in mammals. Collectively, our results implicate synaptic function as a central target in p53-dependent protection from neurodegeneration.

overall_design: 4 samples: tau vs. control

first: Paola

last: Merlo

first: Shouyong

last: Peng

first: Yawei

last: Yang

first: Mel

last: Feany


title: The bZIP transcription factor Atf1 governs the oxidative stress response and sexual differentiation of Cryptococcus neoformans downstream of the HOG pathway

status: Public on Jan 13 2015

city: Seoul

first: Dong-Hoon

address: Yonsei-ro 50

country: South Korea

institute: Yonsei University

summary: The high osmolarity glycerol response (HOG) pathway plays a pivotal role in the stress response, virulence regulation, and differentiation of fungi, including Cryptococcus neoformans that causes fatal meningoencephalitis. Core signaling components of in the HOG pathway, including the Tco-Ypd1-Ssk1 phosphorelay system and the Ssk2-Pbs2-Hog1 MAPK module, have been elucidated but its downstream transcription factors remain unclear. Here we demonstrated that Atf1 with a basic leucine zipper domain is the transcription factor downstream of Hog1 in C. neoformans. We found that ATF1 expression was differentially regulated by oxidative damaging agents, mainly in a Hog1-dependent, but Mpk1-independent, manner. Interestingly, Atf1 not only promoted oxidative stress response and adaptation, but also played an opposing role to Hog1 in the process. Atf1 primarily localized to the nucleus under both unstressed and oxidative stress conditions in a Hog1-independent manner. Our data demonstrated that Atf1 promoted pheromone production and sexual differentiation under negative control by Hog1. Finally, a DNA microarray-based transcriptome analysis of the atf1∆ mutant under unstressed and oxidative stress conditions revealed that Atf1 regulated oxidative stress response genes, including a sulfiredoxin gene (SRX1). Intriguing, the array data further demonstrated that Atf1 modulated basal expression of genes involved in DNA repair and genotoxic stress response. Supporting this, we found that the atf1∆ mutant was highly sensitive to genotoxic agents. In conclusion, this study provided a further insight into the Hog1-dependent oxidative and genotoxic stress response and differentiation mechanism of C. neoformans.

overall_design: There are more than 95% of genome homology between JEC21 and H99. Therefore 6 slides of JEC21 (Cryptococcus neoformans var. neoformans serotype D) 70-mer oligo are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted 2 conditions (with or without treatment of Hydroten peroxide) from H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A), and atf1Δ). We use the mixed all of total RNAs from this experiment as a control RNA. We use Cy3 as Sample dye and Cy5 as a control dye.

first: Shinae

last: Maeng

first: Je-Hyun

last: Ji

first: Anna

last: Floyd

first: Joseph

last: Heitman

first: Yong-Sun

last: Bahn


title: WDLPS and DDLPS aCGH case 73

status: Public on Jan 01 2015

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

summary: these are successive array CGH analyses of a case of retroperitonaeal well-differentiated liposarcoma and its four successive dedifferentiated liposarcoma relapses. We observed differences and similarities between the 5 components

overall_design: The samples were extracted from fresh or formalin fixed-paraffine embedded fragments and were analysed by arrayCGH with nimblegen CGX or Agilent SureTag method. We compared whole genome profiles.

first: Esma

last: Saada

first: Thibaut

last: Fabas

first: Annie

last: Peyron

first: Laurence

last: Bianchini

first: Florence

last: Pedeutour


title: Gonadal transcriptome analysis of wild contaminated female European eels during artificial gonad maturation

city: Arcachon

first: lucie

last: baillon

address: place du docteur Peyneau

institute: université de Bordeaux UMR ePOC

summary: Since the early 1980s, the population of European eels (Anguilla anguilla) has dramatically declined. Nowadays, the European eel is listed on the red list of threatened species (IUCN Red List) and is considered as critically endangered of extinction. Pollution is one of the explanations of the collapse of this species. Among their possible effects, pollutants gradually accumulated in eels during their somatic growth phase (yellow eel stage) would be remobilized during their reproductive migration leading to potential toxic events in gonads. The aim of this study was to investigate the potential effect of pollution on the gonad development of wild female silver eels. Female silver eels from two sites with differing contamination levels were artificially matured. Transcriptomic analyses by means of a 1000 candidate gene cDNA microarray were performed on gonads after 11 weeks of maturation. The results showed that the transcription levels of several genes that were associated to the gonadosomatic index (GSI) were involved in mitotic cell division but also in spermatogenesis. Genes associated to pollution were mainly involved in the mechanisms of protection against oxidative stress, in DNA repair, in the purinergic signaling pathway and in steroidogenesis, suggesting an impairment of gonad development in eels from the polluted site. This was in agreement with the fact that eels from the reference site showed a higher gonad growth in comparison to contaminated fish.

platform_organism:
Anguilla anguilla
Anguilla rostrata

overall_design: Comparison between wild european eels from a clean (Certes) and contaminated site (Gironde) were performed using a common reference (named in raw data reference, colored with cyanine 5)  on microarray.

first: Lucie

last: Baillon

first: Fabien

last: Pierron

first: Jennifer

last: Oses

first: Sarah

last: Bureau du Colombier

first: Antoine

last: Caron

first: Eric

last: Normandeau

first: Patrick

last: Lambert

first: Patrice

last: Couture

first: Pierre

last: Labadie

first: Hélène

last: Budzinski

first: Sylvie

last: Dufour

first: Louis

last: Bernatchez

first: Magalie

last: Baudrimont


title: Polysome profiling of glp-4 mutant animals

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

summary: To determine the translational status of mRNAs in glp-4 mutant animals, we analyzed total and polysomal RNA levels by tiling arrays

overall_design: A total of 8 samples was analyzed (quadruplicates of glp-4_total and glp-4_polysomal, respectively)

first: Claudia

last: Scheckel

first: Stephane

last: Thiry

first: Jane

middle: E

last: Wright

first: Rafal

last: Ciosk


title: Oxidative stress management in Dinoroseobacter shibae: Role of extrachromosomal elements and the importance of a small chromid during starvation

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

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

summary: Aerobic anoxygenic phototrophic bacteria (AAPs) of the Roseobacter group are abundant in the photic zone of the marine environment. Dinoroseobacter shibae, a typical representative, converts light into additional energy that enhances its survival under nutrient-depletion. AAPs produce cytotoxic singlet oxygenunder light exposition, but D. shibae developed mechanisms to counteract the lethal effects of illumination. Recent studies documented a pivotal role of extrachromosomal elements (ECRs) for the ecological fitness of roseobacters, and here we investigated their significance for the adaptation to specific environmental stress. D. shibae possessing five ECRs, i.e. three chromids and two plasmids, was starved for four weeks in the dark and light/dark cycles and the survival strategy was evaluated using transcriptomics. Few genes on the chromosome showed differential expression between non-starved and starved cells, in particular those with a role in oxidative stress response and photosynthesis. Extrachromosomal genes in contrast showed a systematic loss of transcriptional activity, especially in the dark starved cells. The observed silencing of gene expression was not due to plasmid loss, because all five ECRs were stably maintained. Exceptionally, the smallest 72-kb replicon was the least downregulated, and one region with genes for singlet oxygen stress response was even strongly activated under light/dark cycle. A ?72-kb curing mutant completely lost the ability to benefit from AAP under starvation, and we could thus document the essential role of the 72-kb chromid to light-stress adaptation. . Our data moreover suggest that the four ECRs of D. shibae without a vital function are transcriptionally silenced under starvation.

sample_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Loop-design, two biological replicates of D. shibae DFL12T cultivated in artificial salt water medium with succinate as carbon source and 12/12 light-dark cycles. After reaching stationary phase the cells were starved for 4 weeks in the dark or under light-dark cycle.

first: Maya

last: Soora

first: Hui

last: Wang

first: Jörn

last: Petersen

first: Bert

last: Engelen

first: Irene

last: Wagner-Döbler

first: Heribert

last: Cypionka


title: Whole genome miRNA expression profiling using HeLa cells in response to Heat shock stress.

city: New Delhi

first: Mitali

last: Mukerji

state: New Delhi

address: Sukhdev Vihar, Mathura Road

department: Functional Genomics and Molecular Medicine

institute: CSIR-Institute Of Genomics and Integrative Biology

summary: Exiqon miRNA array contains LNA-modified oligos which minimizes the Tm-range within which probe hybridizes with the transcript in query, thus minimizing the mis-match. Taking advantage of this, we used the miRCURY LNA array to investigate genome wide signatures for miRNA expression in response to heat shock stress. We also did mRNA expression profiling using the same RNA to look for possible miRNA-mRNA interaction in response to heat shock stress. For the differentially expressed miRNAs, target predictions were done using both miRanda and TargetScan. The consensus set was used for subsequent experimental validation.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: In total, 6 comparative hybridizations of heat-shock treated versus control were profiled using the Exiqon arrays. These consisted of 3 biological replicates, each with its dye-swap pair.

first: Rajesh

last: Pandey

first: Amit

last: Mandal


title: Transcriptional analysis of Bacillus cereus ATCC 14579 and its ccpA deletion strain grown with and without glucose

status: Public on Jan 05 2015

city: Wageningen

first: Janneke

last: Wijman

address: Bomenweg 2

country: Netherlands

institute: Wageningen UR

summary: The influence of the presence of glucose in the Y1 growth medium of Bacillus cereus strain ATCC 14579 was studied by transcriptional analysis. Furthermore, the role of CcpA in glucose induction or repression of gene expression was assessed by use of a ccpA deletion strain. In total, 300 genes were glucose repressed and 173 genes glucose activated. For 212 genes the glucose repression was clearly CcpA dependent, whereas for 116 genes CcpA dependent glucose induction was observed. Functional analysis of the glucose regulated genes showed these genes mainly to be involve in energy production and conversion and in metabolism. Furthermore, genes that were glucose repressed were shown to be involved in cell motility.

overall_design:
The wild type and its ccpA deletion strain were grown with and without 0.5% glucose in Y1. Comparisons performed were:
1. wild type and ccpA deletion strain with glucose
2. wild type and ccpA deletion strain without glucose
3. wild type with and wild type without glucose
4. ccpA deletion strain with and ccpA deletion strain without glucose.
The experiments were performed in duplicate and the duplicate samples were hybridised with a dye-swap.

first: Tjakko

last: Abee

first: Menno

last: van der Voort


title: Development of miRNA expression signatures of MEFs deficient in a ER stress mediator XBP1 for tunicamycin treatment

first: Seiichi

last: Oyadomari

summary: To further development of our miRNA expression approach to ER stress, we have employed miRNA microarray expression profiling as a discovery platform to identify ER stress-responsible ones.   Mouse embryonic fibroblasts (MEFs) deficient in a ER stress mediator XBP1 were treated with tunicamycin for 12 or 24 hrs. miRNAs responsible for tunicamycin-treatment for 12hrs in XBP1-dependent manner were extracted. Among them, expression of three miRNAs (miR-23a, miR-27a, miR-24-2) was quantified in the RNA samples from  the same as the microarray, and COS7 cells by real-time PCR, confirming existence of similar mechanisms of trancriptional repression in ER stress by tunicamycin treatment.

overall_design: Mouse embryonic fibroblasts (MEFs) deficient in a ER stress mediator XBP1 were treated with 2ug/mL tunicamycin for 12 or 24 hrs. Two independent experiments were performed at each time (untreated, 12 or 24 hrs). miRNAs responsible for tunicamycin-treatment for 12hrs in XBP1-dependent manner were extracted.

first: Taiji

last: Ito

first: Tomoko

last: Mori

first: Robert

last: Zheng

first: Chinobu

last: Miyamoto

first: Kazue

last: Tsugawa

first: Kiyoe

last: Kurahashi

first: Mari

last: Funahashi

first: Ryosuke

last: Sato

first: Naoko

last: Miura

first: Kazuna

last: Takahara

first: Miho

first: Masato

last: Miyake


title: Complement Roles Revealed by Immune Gene Profiling in Endometriosis and Endometriosis-Associated Ovarian Cancer

status: Public on Jan 07 2015

city: Pittsburgh

first: SungHwan

last: Kim

address: 200 Lothrop, BST W1200

institute: University of Pittsburgh

summary: Mechanisms of immune dysregulation against established tumors are relatively well understood. Much less is known about the role of immune effectors against cancer precursor lesions. Endometrioid and clear cell ovarian tumors may partly derive from endometriosis, a commonly diagnosed chronic inflammatory disease. We performed here the most comprehensive immune gene expression analysis of pelvic inflammation in endometriosis and endometriosis-associated ovarian cancer (EAOC).

overall_design:
RNA was extracted from 120 paraffin tissue blocks comprising of normal endometrium (n=32), benign endometriosis (n=30), atypical endometriosis (n=15) and EAOC (n=43). Serous tumors (n=15) were included as non-endometriosis associated controls. The immune microenvironment was profiled using Nanostring and the nCounter® GX Human Immunology Kit, comprising probes for a total of 511 immune genes.

Please note that 3 normal endometrium samples did not pass the array quality filtering and therefore excluded in the data analyses.

first: Anda

middle: M

last: Vlad


title: Gene transcription profiling in wild and laboratory-exposed eels reveals common responses to low temperature and chronic pollution exposure

first: lucie

last: baillon

summary: Aquatic ecosystems are subjected to a variety of man-induced stressors but also vary spatially and temporally due to variation in natural factors. In such complex environments, it remains difficult for ecotoxicologists to evaluate the effects of contaminants in wild organisms. The aim of the present study was to test the possibility to detect and unravel the effects of different anthropogenic and natural factors on wild fish by the use of a DNA microarray. Transcriptomic profiles from laboratory-exposed and wild fish sampled along a contamination gradient were compared. During laboratory experiments, fish were exposed to pollutants or natural factors under levels that were closed to those found in the sampling sites. A strong difference was observed between the transcriptomic patterns of wild and laboratory-exposed animals, suggesting a general stress induced by captivity in laboratory. Surprisingly, animals acclimatized to cold temperature clustered with fish from the most contaminated sites and shared common genes involved notably in epigenetic mechanisms. A possible energy saving strategy was suggested in cold-acclimated animals. This result may suggest that animals chronically exposed to contaminants develop a general defense/adaptation strategy against pollution through a general shunt in their basal metabolism, whatever the type of contaminants.

sample_organism:
Anguilla anguilla
Anguilla rostrata

overall_design: 84 samples were analyzed from wild and laboratory animals (5 individuals per condition or sampling site). Seven sampling wild sites were selected in Canada (St. Jean, Sud-Ouest, St. François, St. Pierre) and in France (Dordogne, Garonne, Gironde) on the basis of their known gradient of contamination by metallic and organic pollutants previously described in Baillon et al., in press. Each sample were hybridized with a same reference on array (30 samples from reference site (Certes, France) collected in spring 2011 and 2012. Animals from laboratory exposures were described below.

first: Lucie

last: Baillon

first: Fabien

last: Pierron

first: Pauline

last: Pannetier

first: Eric

last: Normandeau

first: Pierre

last: Labadie

first: Hélène

last: Budzinski

first: Patrick

last: Lambert

first: Patrice

last: Couture

first: Louis

last: Bernatchez

first: Magalie

last: Baudrimont


title: Development of miRNA expression signatures of MEFs deficient in a ER stress mediator ATF6a for tunicamycin treatment

first: Seiichi

last: Oyadomari

summary: To further development of our miRNA expression approach to ER stress, we have employed miRNA microarray expression profiling as a discovery platform to identify ER stress-responsible ones.   Mouse embryonic fibroblasts (MEFs) deficient in a ER stress mediator ATF6a were treated with tunicamycin for 12 or 24 hrs. miRNAs responsible for tunicamycin-treatment for 12hrs in ATF6a-dependent manner were extracted. Among them, expression of three miRNAs (miR-26a, miR-27b, miR-143) was quantified in the RNA samples from  the same as the microarray by real-time PCR.

overall_design: Mouse embryonic fibroblasts (MEFs) deficient in a ER stress mediator ATF6a were treated with 2ug/mL tunicamycin for 12 or 24 hrs. Two independent experiments were performed at each time (untreated, 12 or 24 hrs). miRNAs responsible for tunicamycin-treatment for 12hrs in ATF6a-dependent manner were extracted.

first: Taiji

last: Ito

first: Tomoko

last: Mori

first: Robert

last: Zheng

first: Chinobu

last: Miyamoto

first: Kazue

last: Tsugawa

first: Kiyoe

last: Kurahashi

first: Mari

last: Funahashi

first: Ryosuke

last: Sato

first: Naoko


title: Microarray analysis of the Asian seabass (Lates calcarifer) brains

city: Singapore

first: Junhui

last: Jiang

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: In this study, we attempt to characterize the transcriptomic profile of the Asian seabass brains collected from the male and female sexes. The objective is to identify genes that show sexually dimorphic expression in the brain of this species.   For this experiment, Asian seabass were collected from the Marine Aquaculture Center of the Agri-Food & Veterinary Authority of Singapore. There were no treatments carried out in this experiment. Four brains from adult male seabass (5 years old) with M3-type testis and four brains from adult female seabass (5 years old) with F3-type ovaries were used in this experiment. (Gonads were examined by histology and classified according to sexual maturation status as described by Guiguen and colleagues (Guiguen et al. Environmental Biology of Fishes, 1994)).

overall_design:
Total 8 samples.
Male Brain : 4
Female Brain : 4

first: Laszlo

last: Orban


title: BAC aCGH profiling of 64 GBM (primary & recurrent)

city: Acton

first: Sebastian

last: Kurscheid

state: ACT

address: 57 Garran Road

department: JCSMR

country: Australia

institute: Australian National University

summary: aCGH was used to profile copy-number aberrations (CNA) in 64 glioblastoma specimen of patients treated within clinical trials. The data was used to identify changes in CNA which contribute to the aberrant of expression of HOX transcription factors. Our group had previously demonstrated that expression of HOX genes was associated with increased resistance to chemo-radiotherapy and worse outcome in GBM patients  Keywords: Disease state comparison

overall_design: Genomic DNA from the 64 samples and synthetic normal reference DNA were labelled with Cy3 and Cy5 respectively and hybridised to HumArray3 and HumArray2 chips. The unified platform HumArray3.1 is used for annotation purposes

first: Pierre

last: Bady

first: Marie-France

last: Hamou

first: Annie-Claire

last: Diserens

first: Roger

last: Stupp

first: Mauro

last: Delorenzi

first: Monika

last: Hegi


title: Microarray analysis of the Asian seabass (Lates calcarifer) gonads

summary: In this study, we attempt to characterize the transcriptomic profile of the Asian seabass gonads at various developmental stages. The protandric Asian seabass or barramundi (Lates calcarifer) typically matures as a male at approximately 2–4 years of age and then changes sex to a female in later years. For this experiment, Asian seabass of several ages were collected from the Marine Aquaculture Center of the Agri-Food & Veterinary Authority of Singapore and from farms around Singapore. There were no treatments carried out in this experiment. The gonads were examined by histology and classified according to sexual maturation status as described by Guiguen and colleagues (Guiguen et al. Environmental Biology of Fishes, 1994). Altogether, we analyzed 22 gonadal samples that could be classified into six different types of gonads.

overall_design:
Total 22 samples:
Adult Ovaries (F3-stage; 5 years old fish) : 4
Adult Testes (M3-stage; 5 years old fish) : 4
Early Testes (M3-stage; 8-9 months old fish) : 3
Early Transforming Gonads (>2 years old fish) : 3
Late Transforming Gonads (>2 years old fish) : 4
Undifferentiated Gonads (4.5 months old fish) : 4


title: Effect of Pro- and anti-inflammatory lipids in intracellular survival and killing of mycobacteria

city: Heidelberg

first: Jonathon

last: Blake

state: BW

address: Meyerhofstr 1

institute: EMBL

summary:
Mouse macrophages J774A.1 were pre-treated with the anti-inflammatory lipid eicosapenaenoic acid (EPA) or the pro-inflammatory lipid ceramide (Cer) for 3h.
Macrophages were then infected with Mycobacterium smegmatis for 1h, and total RNA was collected. In a parallel experiment, infected macrophages were infected for 1h, 4h and 24h. At these time points, macrophages were lysed, bacteria was collected and quantified by the Colony Forming Units (CFU) Assay. This provided the kinetics of the killing of Mycobacteria inside mouse macrophages. CFU experiments revealed that cells pre-treated with EPA showed an increased number of bacteria inside macrophages, in contrast to cells pre-treated with Cer. To dissect the molecular mechanisms involved in the survival and killing of mycobacteria infected macrophages, mediated by lipids, gene expression studies were performed.

overall_design: Cultures of Mycobacterium smegmatis mc2155 harbouring a p19-(long lived) EGFP plasmid were grown to exponential growth phase. Bacteria were pelleted, washed in PBS and resuspended in medium DMEM with a multiplicity of infection (MOI) of 10 (10 bacteria per macrophage). Clumps of bacteria were removed by ultrasonic treatment of bacterial suspensions in an ultrasonic water bath for 15 minutes, followed by a low speed centrifugation for 2 minutes.   Mouse macrophages J774A.1 were pre-.treated with the anti-inflammatory lipid eicosapenaenoic acid (EPA) or the pro-inflammatory lipid ceramide (Cer), 3h before infection. Mouse macrophages J774A.1 were infected with Mycobacterium smegmatis mc2155 for 1h, at 37ºC and 5% CO2.   After 1h of infection, cells were washed with PBS. After washing, 1 ml Trizol was added per well, to collect total RNA.  The experimental condition were:   samples 1.1, 1.2, 1.3: Untreated macrophages;  samples 2.1, 2.2, 2.3: Mock treated macrophages (ethanol 1ul/ml);  samples 3.1, 3.2, 3.3: EPA (15uM) treated macrophages (ethanol 1ul/ml);  samples 4.1, 4.2, 4.3: Cer (5ug/ml)  treated macrophages (ethanol 1ul/ml);  samples 5.1, 5.2, 5.3: Untreated macrophages, infected with Mycobacterium smegmatis mc2155 for 1h;  samples 6.1, 6.2, 6.3: Mock treated macrophages (ethanol 1ul/ml) infected with Mycobacterium smegmatis mc2155 for 1h;  samples 7.1, 7.2, 7.3: EPA (15uM) treated macrophages (ethanol 1ul/ml) infected with Mycobacterium smegmatis mc2155 for 1h;  samples 8.1, 8.2, 8.3: Cer (5ug/ml)  treated macrophages (ethanol 1ul/ml) infected with Mycobacterium smegmatis mc2155 for 1h;      In a parallel experiment, infected macrophages remained with the bacteria for 1h, 4h and 24h after infection. After these time points, the macrophages were lysed, the bacteria was collected and quantified by the Colony Forming Units (CFU) Assay. This provided the kinetics of the killing of non-pathogenic intracellular bacteria inside mouse macrophages.  For the CFU assay, after 1h of infection, cells were washed with PBS and Gentamicin (10ug/ml) in DMEM to kill the extracellular bacteria. At discrete time points, cells were washed with PBS and lysed with sterilized water.   Quantitative cultures of bacteria were performed in a 10-fold serial dilutions, inoculated on 7H10 agar plates. 5ul were plated in triplicate and the number of colonies were counted after 48h.

first: Paulo

last: Bettencourt

first: Gareth

last: Griffiths

first: Elsa

last: Anes


title: MiRNA profiling in Rattus norvegicus pancreatic cells: INS-1E cells during infection with Coxsackie B4 virus

city: Shatin, New Territories

first: Wai Yip

last: Lam

address: Area 39, Lo Kwee-Seong Integrated Biomedical Sciences Building

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: This study aims at elucidating how Coxsackie B virus infection perturbs the host's miRNA regulatory pathways that may lead to different pathological events using the miRNA microarray approach.

overall_design: The rat pancreatic cell line - INS-1E, was infected with various preparations of Coxsackie B4 viruses was analysed for miRNA expression profiles subsequently. The miRNA expression profiles were measured at 48, and 72 hours post infection, respectively.

first: W

middle: Y


title: MiRNA profiling in Rattus norvegicus pancreatic cells: RIN-5F cells during infection with Coxsackie B4 virus

overall_design: The rat pancreatic cell line -RIN-5F, was infected with various preparations of Coxsackie B4 viruses was analysed for miRNA expression profiles subsequently. The miRNA expression profiles were measured at 48, and 72 hours post infection, respectively.


title: MiRNA profiling in Rattus norvegicus pancreatic cells

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

overall_design: Refer to individual Series


title: Aspergillus nidulans strains TNO2A3, ∆msbA and ∆MHD grown in complete media (YUU) and on avicel as sole carbon source

city: Ribeirao Preto

first: Neil

last: Brown

address: Av. do Cafe

institute: USP

summary: Transcriptome of A. nidulans TNO2A3, ∆msbA and ∆MHD strains when grown on complete media (YUU) and transferred to minimal media plus avicel as a sole carbon source for 24 hours

overall_design: Two conditions: complete media (reference) for 24h and minimal media plus avicel for 24 hours. Three strains TNO2A3, ∆msbA and ∆MHD. Three biological repetitions of each point.

first: Gustavo

last: Goldman


title: CRTC1 overexpression in Caco-2 colon cancer cells

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary: To evaluate the genes differentially regulated by CRTC1 in colonic epithelial tumor.

overall_design: Subconfluent Caco-2 cells were transfected with 200ng of CRTC1 expression plasmid or corresponding empty vector (pBS) overnight. N = 4 per group.

first: Sandra

last: Guilmeau


title: Suppression of BRCA1 sensitizes to proteasome inhibitors in DNA repair-independent manner.

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary:
Germline and somatic mutations in BRCA1predispose to breast cancer. We found that proteasome inhibitors can selectively kill BRCA1-depleted cells. The toxic response involves a deregulation of the G1/S cell cycle checkpoint via hyperphosphorylation of RB1,  53BP1-mediated arrest at G2/M checkpoint, and ERN1-mediated unfolded protein response, culminating in a TNF receptor-mediated apoptosis. The study new unexpected molecular functions for BRCA1 protein and opens a novel possibility for the treatment of BRCA1-deficient cancers.
We used microarrays to detail the global programme of gene expression underlying the response of BRCA1-deficient cells to proteasome inhibitor bortezomib.

overall_design: We aimed to identify genes that are strongly up- or down-regulated with a combination of BRCA1 knockdown and proteasome inhibition, but none of these treatments alone before the onset of apoptosis. HeLa and U2OS cells were transfected either with a non-targeting or anti-BRCA1 siRNAs (siControl or siBRCA1, respectively), treated with bortezomib for 8 hours, after which RNA was extracted for hybridization on Affymetrix microarray. The following treatments have been performed: (T1) siControl; (T2) siControl + 20 nM bortezomib for 8h; (T3) siBRCA1; (T4) siBRCA1 + 20 nM bortezomib for 8h. All samples were used without replicas. However, all genes showing inconsistent expression pattern between the two cell lines were excluded from further consideration. Selected candidate genes were subject to validation by qRT-PCR.

first: Yuexi

last: Gu

first: Peter

last: Bouwman

first: Jani

last: Saarela

first: Jos

last: Jonkers

first: Sergey

last: Kuznetsov


title: Comparative analysis of chrysanthemum transcriptome in response to infection of three viruses: Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

summary: Gene expression analysis of chrysanthemum infected with three different viruses including Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X have been performed using the chrysanthemum 135K microarray.

overall_design: Mock and each virus infected chrysanthemum plants were subjected for microarray analysis.

first: H

last: Choi

first: Y

last: Jo

first: K

last: Cho


title: Expression data from LT-HSCs from bone marrow non-irradiated, 8Gy CDR and 8Gy FLASH total body irradiated mice

city: Fontenay-aux-roses

first: Nathalie

last: Gault

address: 18 rue de Panorama

institute: CEA

summary:
Total body irradiation (TBI) of mice using two dose rates, conventional dose rate (CDR) versus flash dose rate (FLASH), induced transient decrease of number of LT-HScs in bone marrow  and a total recovery of these cells 15 days after TBI
We used microarrays to detail the global programme of gene expression underlying the recovery of LT-HSCs and identified distinct classes of up or down- regulated genes according the modality of irradiation

overall_design: LT-HScs were isolated  from bone marrow of non-irradiated, 8Gy CDR and 8Gy FLASH irradiated mice 15 days post-TBI for RNA extraction and hybridization on affymetrix microarrays.

first: Marie-Catherine

last: Vozenin


title: Calcitriol Induces Endoplasmic Reticulum Stress Response in Breast Cancer Cells

city: Bornova

first: Hikmet

middle: Hakan

last: Aydin

state: Izmir

department: Department of Medical Biochemistry

country: Turkey

institute: Ege University School of Medicine

summary:
Effects of calcitriol on expressions of ER stress related genes were evaluated with microarray.
Calcitriol, the active form of vitamin D, is known to induce apoptosis in cancer cells and increase intracellular calcium. Increase in cytopalsmic calcicium levels may indicate a decrease in endoplasmic reticulum (ER) calcium levels since ER is the main storage unit for calcium. Decrease in ER calcium levels are known to induce ER stress which can lead to apoptosis. However the effects of calcitriol on ER stress have not been reported before. Here we hypotesized that the cellular effects of calcitriol can be explained by induction of ER stress. We have tested this hypothesis by assessing calcitriol induced transcriptomic alterations with a focus on ER stress related genes.

overall_design: We analyzed MCF-7 and MDA-MB-231 cells treated with calcitriol or DMSO (Each group consists of 3 replicates) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Partek Genomic Suite. No technical replicates were performed.

first: Ali

last: Ozkaya

first: Ela

last: Haddur

first: Handan

last: Ak

middle: H


title: Functional analysis of the cytoprotective transcription factor Nrf2 in keratinocytes: Identification of Nrf2-regulated miRNAs

city: Manchester

first: Svitlana

last: Kurinna

address: Dover Street

country: United Kingdom

institute: University of Manchester

summary:
Nrf2-regulated mRNAs are known; however, no Nrf2-regulated miRs have been identified
miR microarray analysis from total RNA samples was performed to test which miRs are regulated by Nrf2

overall_design: Total RNA from skin of mice with constitutively active Nrf2 (CMV-caNrf2), dominant-negative Nrf2 (dnNrf2), and correcponding control littermates (K5Cre(wt) for CMV-caNrf2 and wt for dnNrf2)

first: Sabine

last: Werner


title: Development of a 44K custom oligo microarray using 454 pyrosequencing data for large scale gene expression analysis in tea plant (Camellia sinensis)

city: Hangzhou

first: Lu

last: Wang

state: Zhejiang

address: 9th, South Meiling Road

country: China

summary: To investigate the large-scale gene expression in different tea clones, a custom oligo microarray was developed using sequences from RNA-seq for probe designing. We succeeded in developing a tea oligo microarray resource which can be successfully used to analyze gene expression in any tea clones without the need for prior sequence knowlege.

overall_design: A 4×44K microarray consisting of 43833 in situ synthesized 60-mer oligonucleotide probes using the 42440 unigene sequences from RNA-seq was designed. Gene expression in leaves was detected in the four tea cultivars using the microarray. Four tea plant cultivars, Longjing 43, Zhongcha 108, Zhonghuang 1 and Zhonghuang 2 were grown in the China National Germplasm Hangzhou Tea Repository (CNGHTR) at the Tea Research Institute, Chinese Academy of Agricultural Sciences (TRI, CAAS). The experiment of microarray analysis included three biological replicates for each cultivar.

first: Xinchao

first: Chuan

last: Yue

first: Hongli

last: Cao

first: Yanhua

last: Zhou

first: Yajun

last: Yang


title: Hydrogen production experiment in Chlamydomonas induced by sulfur starvation

city: Bielefeld

first: Jörg

last: Toepel

address: Universitätsstrasse 27

department: Biology

institute: University of Bielefeld

summary: Comparison of gene expression for chlamydomonas cells grown for 24h, 48h 72h, 96h in sulfur depleted media

overall_design: Two-condition experiment,   3 Biological replicates


city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

department: Biological Sciences

country: USA

institute: University of Alabama in Huntsville

summary:
Local adaptation can play a fundamental role in the isolation of populations. While less well-studied than differentiation in sequence variation, changes in transcriptional variation during speciation also are fundamental to the evolutionary process. Drosophila mojavensis offers an unprecedented opportunity to examine the role of transcriptional differentiation in local adaptation. Drosophila mojavensis is a cactophilic fly composed of four ecologically distinct subspecies that inhabit the deserts of western North America. Each of the four subspecies utilizes necrotic tissue of different cactus host species characterized by distinct chemical profiles. The subspecies in Baja California, Mexico uses Stenocereus gummosus (Agria), in mainland Sonora it uses S. thurberi (Organ Pipe), in the Mojave Desert the host is Ferocactus cylindraceus (Red Barrel) and in Santa Catalina Island, USA, Opuntia littoralis (Prickly Pear) is the host. In this chapter we examine how the adaptation to the different environmental conditions across the four subspecies have shaped their transcriptional profiles. Using complete D. mojavensis genome microarrays we examined the transcriptome of third instar larvae from all four subspecies reared in standard laboratory media free of necrotic cactus-derived compounds. This experimental strategy focused on differences between constitutively expressed genes and not genes induced by necrotic cactus-derived compounds. The subspecies exhibited significant differential expression of genes that likely underlie the adaptation to different cactus hosts, such as detoxification genes (Glutathione S-transferases, Cytochrome P450s and UDP-Glycosyltransferases) and chemosensory genes (Odorant Receptors, Gustatory Receptors and Odorant Binding Proteins).
Dataset from Matzkin, L. M. and Markow, T.A.  Transcriptional differentiation across the four cactus host races of Drosophila mojavensis. In Speciation: Natural Processes, Genetics and Biodiversity.  Edited by Michalak, P.  Nova Science Publishers, Inc.

sample_organism:
Drosophila mojavensis
Drosophila mojavensis mojavensis
Drosophila mojavensis sonorensis
Drosophila mojavensis wrigleyi

overall_design: The comparisons was between the four subspecies of D. mojavensis.  A total of 22 isofemales lines were analyzed in duplicate.

first: Therese

last: Markow


title: Murine E14,5 DRGs: TrkAC-KI vs. Wild type

city: Marseille

first: Aziz

last: Moqrich

address: case 907, campus de luminy

institute: CNRS

summary: Transcriptional profiling of embryonic DRG neurons from TrkAC-KI and wild type mice.

overall_design: Two-condition experiment, TrkAC-KI vs. Wild type. Three independent biological replicates, each containing DRGs from 6-8 embryos from multiple litters, were prepared for each genotype.

first: Svetlana

last: Gorokhova

first: Stéphane

last: Gaillard

first: Pascale

last: Malapert

first: Wassim

last: Legha

first: Grégory

last: Baronian

first: Jean-Pierre

last: Desvignes

first: Serge

last: Alonso


title: Evasion of Mucosal Defenses During Aeromonas hydrophila Infection of Channel Catfish (Ictalurus puncatus) Skin

city: AUBURN

first: chao

last: li

address: 203 swingle hall

institute: auburn university

summary: The mucosal surfaces of fish serve as the first-line of defense against the myriad of aquatic pathogens present in the aquatic environment. The immune repertoire functioning at these interfaces is still poorly understood. The skin, in particular, must process signals from several fronts, sensing and integrating environmental, nutritional, social, and health cues. Pathogen invasion can disrupt this delicate homeostasis with profound impacts on signaling throughout the organism. Here, we investigated the transcriptional effects of virulent A. hydrophila infection in channel catfish skin, Ictalurus punctatus. We utilized an 8X60K Agilent microarray to examine gene expression profiles at critical early timepoints following challenge—2 h, 8 h, and 12 h. Expression of a total of 2,168 unique genes was significantly perturbed during at least one timepoint. We observed dysregulation of a number of genes involved in antioxidant, cytoskeletal, immune, junctional, and nervous system pathways.  In particular, A. hydrophila infection rapidly altered a number potentially critical lectins, chemokines, interleukins, and other mucosal factors in a manner predicted to enhance its ability to adhere and invade the catfish host.

overall_design: Two-condition experiment, control vs. infected skin. Biological replicates: 3 control replicates, 3 infected replicates. 3 timepoints.

first: Chao

last: Li

first: Ruijia

first: Baofeng

last: Su

first: Yupeng

last: Luo

first: Benjamin

last: Beck

first: Eric

last: Peatman


city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Cellular active small molecule inhibitors of Mycobacterium tuberculosis by NMR fragment screen.

overall_design: Microarray experiments were performed as dual-color hybridizations on reporter level. In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed. Two different labeling methods were applied. RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies) using FullSpectrum MultiStart Primer for T7 IVT RNA Amplification (BioCat GmbH, Heidelberg, Germany) as random T7 labeling. Alternatively, the total RNA samples were amplified with the TransPlex Whole Transcriptome Amplification Kit (Sigma-Aldrich, Munich, Germany) and labeled with BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen, Karlsruhe, Germany) as WTA BioPrime indirect. Both methods were combined in the data analysis and only results derived from both labeling methods were considered as relevant for further verification.

first: Stefan

last: Kaufmann

first: Thulassi

last: Warrier


title: Circulating microRNA Signatures in Mice Exposed to Lipoteichoic acid

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: To profile the expression of circulating microRNAs (miRNAs) of mice in exposure to intraperitoneal lipoteichoic acid (LTA) injection and compare that with those with lipopolysaccharide (LPS) injection

overall_design: C57BL/6 mice received intraperitoneal injections of 100 μg of LTA originated from Bacillus subtilis, Streptococcus faecalis, and Staphylococcus aureus were killed 6 h and the whole blood samples were obtained for miRNA expression analysis using a miRNA array

first: Johnson

middle: C

last: Yang

first: Cheng-Shyuan

last: Rau


title: Ambion and Exiqon miRNA profiling

country: Germany

summary: Influenza A virus induces endogenous miR-141 to undermine MxA antiviral activity

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
color-swap dye-reversal
In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed. Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 2-fold change expression cut-off for ratio experiments was applied together with anti-correlation of color-swapped ratio profiles was applied, rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

first: Alexander

last: Karlas

first: Hany

last: Khalil

first: Thomas

middle: F

last: Meyer


title: MicroRNAs Regulate p21Waf1/Cip1 Protein Expression and the DNA Damage Response in Human Embryonic Stem Cells

city: Brno

first: Marek

last: Mraz

address: Cernopolni 9

department: Dept. Hematology and Oncology

institute: University Hospital Brno

summary: Studies of human embryonic stem cells (hESCs) commonly describe the non-functional p53-p21 axis of the G1/S checkpoint pathway with subsequent relevance for cell cycle regulation and the DNA damage response (DDR). Importantly, p21 mRNA is clearly present and upregulated after the DDR in hESCs but p21 protein is not detectable. In this article, we provide evidence that expression of p21 protein is directly regulated by the microRNA pathway under standard culture conditions and after DNA damage. The DDR in hESCs leads to upregulation of tens of microRNAs, including hESC-specific microRNAs such as those of the miR-302 family, miR-371-372 family, or C19MC microRNA cluster. Most importantly, we show that the hESC-enriched microRNA family miR-302 (miR-302a, miR-302b, miR-302c, and miR-302d) directly contributes to regulation of p21 expression in hESCs and thus demonstrate a novel function for miR-302s in hESCS. The described mechanism elucidates the role of microRNAs in regulation of important molecular pathway governing the G1/S transition checkpoint before as well as after DNA damage.

overall_design:
Karyotypically normal hESC lines CCTL-14 (46, XX, at passages 20–30 and 242–250, respectively) was used in this study (for detailed characterization of hESC lines see International Stem Cell Registry: http://www.iscr-admin). For UVC irradiation, culture media were aspirated and cells were washed once with phosphate-buffered saline (PBS) without Mg2+ and Ca2+ (pH 7.4). For each time point, nine culture dishes were independently irradiated with a dose of 3 J/m2. Cells were then further incubated in culture media (37°C/5% CO2) until they were harvested at 4, 8, and 16 hrs, respectively, post-UVC treatment.

Differentiation and culture of NPCs derived from hESCs
To induce neural differentiation, we utilized a protocol based on embryoid body (EB) formation with simultaneous all-trans-retinoic acid (RA) treatment. Colonies of hESCs were transferred to a non-adherent cell culture dish in the presence of differentiation media [DMEM/F12:Neurobasal 1:1, N2, B27 (Invitrogen), 2 mmol/l L-Glutamine (all media components from Invitrogen, Carlsbad, CA, USA), 1× MEM non-essential amino acids, 0.5% penicillin-streptomycin, 100 µmol/l β-2 mercaptoethanol (Sigma-Aldrich, St. Louis, MO, USA) and 20 ng/ml FGF-2 (PeproTech, Rocky Hill, NJ, USA)]. RA was added (Sigma-Aldrich, concentration 0.5 µmol/l) into fresh differentiation media on days 6, 10, and 14 after the beginning of EB development. On day 16, cells were dissociated using Accutase (Sigma-Aldrich) and plated on a gelatin-coated cell culture dish in maintenance media (DMEM/F12, N2, B27, L-Glutamine, MEM non-essential amino acids, 0.5% penicillin-streptomycin, 100 µmol/l β-2 mercaptoethanol, and 20 ng/ml FGF-2). Cells were passaged twice and subsequently harvested for RNA isolation.

first: Dasa

last: Dolezalova

first: Tomas

last: Barta

first: Karla

last: Plevova

first: Vladimir

last: Vinarsky

first: Zuzana

last: Holubcova

first: Josef

last: Jaros

first: Petr

last: Dvorak

first: Sarka

last: Pospisilova

first: Ales

last: Hampl


title: Formaldehyde stress response in Methylobacterium extorquens AM1

city: Seattle

first: Jonathan

middle: A.

last: Miller

state: WA

address: 616 NE Northlake Place

department: Microbiology

institute: University of Washington

summary: The goal of this study was to use microarrays to identify genes differentially regulated under conditions of formaldehyde stress relative to two other stress conditions (oxidative, osmotic) in an effort to identify genes that might be involved in a formaldehyde-specific stress response, rather than a general stress response, in the model methylotroph Methylobacterium extorquens AM1.

overall_design: Two color experiment, three treatments, three biological replicates per treatment, and two technical (dye swap) replicates per biological replicate: formaldehyde-stressed vs. unstressed cells; oxidative-stressed vs. unstressed cells; and osmotic-stressed vs. unstressed cells.

middle: A

first: Mary

last: Lidstrom


title: The homeoprotein Six2 promotes breast cancer metastasis via transcriptional and epigenetic control of E-cadherin expression

status: Public on Dec 31 2014

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary: Mouse mammary carcinoma cell line 4TO7 was used in this experiment. Six2 overepxression experiment.The mouse Six2 cDNA taken from CMV-sport6 (Open Biosystems) was cloned into a pcDNA3.1-hygromycin vector and transfected into 4TO7 cells, after which stably transfected cells were selected. Gene expression profiles were performed in triplicate for the control and over-expressed lines.

overall_design: six samples, three controls and three replicates with Six2 overexpression.

first: Aik

first: Heide

middle: L

last: Ford

first: Chu-An

last: Wang


title: AIM2 and endosomal TLRs differentially regulate arthritis and autoantibody production in DNase II deficient mice

status: Public on Dec 25 2014

city: Worcester

first: Rebecca

last: Baum

address: 55 N Lake Ave LRB 240D

department: Medicine

institute: University of Massachusetts Medical School

summary: Innate immune PRRs sense nucleic acids from microbes and orchestrate cytokine production to resolve infection. Inappropriate recognition of host nucleic acids also results in autoimmune disease. Here we utilize a model of inflammation resulting from accrual of self DNA (DNase II-/- Ifnar-/-) to understand the role of PRR sensing pathways in arthritis and autoantibody production. Using mice deficient in DNase II/Ifnar together with deficiency in either STING or AIM2 (TKO), we reveal central roles for the STING and AIM2 pathway in arthritis. AIM2 TKO mice show limited inflammasome activation and, like STING TKO mice, have reduced inflammation in joints. Surprisingly, autoantibody production is maintained in AIM2 and STING TKO mice, while DNase II-/- Ifnar-/- mice also deficient in Unc93b, a chaperone required for TLR7/9 endosomal localization, fail to produce autoantibodies to nucleic acids. Collectively, these data support distinct roles for cytosolic and endosomal nucleic acid sensing pathways in disease manifestations.

overall_design: Sera from 3 month-old DKO and STING TKO mice were used (2 samples/genotype) as well as sera from 10 month-old DKO (3 samples), STING TKO (5 samples), AIM2 TKO (4 samples), and Unc93b TKO (3 samples)

first: Shruti

last: Sharma

first: Susan

last: Carpenter

first: Quan-Zhen

last: Li

first: Patricia

last: Busto

first: Katherine

last: Fitzgerald

first: Ann

last: Marshak-Rothstein

first: Ellen

last: Gravallese