title: Effect of maternal age on the granulosa cell transcriptome of preovulatory dominant follicle in cattle

status: Public on Jun 16 2016

city: SASKATOON

first: Muhammad

middle: Irfan-ur-Rehman

last: Khan

state: SASKATCHEWAN

address: 52 Campus drive

department: Veterinary Biomedical Sciences

country: Canada

institute: University of Saskatchewan

summary: The objective of the study was to determine how maternal age influences the transcriptome of the dominant follicle during the preovulatory period. We tested the hypotheses that delayed ovulation in aged cows is associated with 1) altered gene expression of granulosa cells of  preovulatory follicles (24 h after LH treatment) and 2) decreased synthesis of progesterone by  granulosa cells of the preovulatory follicle. Granulosa cells of preovulatory follicles obtained 24 h after LH treatment from aged Hereford cows (19.0 ±2.5 years; n=3) were compared to those from young cows (9.0 ± 0.6 years; n=3) using bovine specific microarrays (EmbryoGENE-EMBV3; GPL13226). Results were confirmed by RT-qPCR. A total of 1340 genes or gene isoforms were expressed differentially (≥2-fold change; p ≤ 0.05) in aged cows vs. young cows (daughters of aged cows). In conclusion, transcriptome analysis of granulosa cells from aged cows revealed a delayed or suboptimal response to the preovulatory LH stimulus, represented by delayed cellular differentiation, luteinization and progesterone synthesis.

overall_design: Granulosa cells of the dominant preovulatory follicle 24 h after LH treatment were compared  between aged vs.young cows. Three biological replicates (each composed of one aged and one young cow). 3 Three technical replicate (dye swap). One biological or technical replicate per array.

middle: I


title: MatA S. cerevisiae cells exposed to Iztli peptide 1 for 3.5, 7, 15 and 30 minutes

status: Public on Jun 28 2016

city: Mexico DF

first: Gabriel

last: Del Rio

state: DF

address: Circuito exterior s/n, Delegacion Coyacan

department: Biochemistry and Structural Biology

country: Mexico

institute: Instituto de Fisiologia Celular, UNAM

summary: Transcriptional profiling of MatA yeast cells exposed to a cationic antimicrobial peptide (Iztli peptide 1) for 3.5, 7, 15 and 30 min is compared with MatA yeast cells without the peptide

overall_design:
Two-condition experiment, MatA cells with peptide (P) and without it (C). Biological samples: 4 control, 4 treatment, independently grown and harvested. Two replicates per array.
Please  note that [1] there is one raw data file per two replicates, as indicated in the sample description field [2] the Columns 10 and 11 (in the raw data file), labeled as Raw intensity (mean) T1C and  Raw intensity (mean) T1P, correspond to the raw intensities for each spot. T1C correspond to control and T1P correspond to treatment with a peptide named Iztli Peptide 1 [3] The replicates can be located by sorting the column standard_name. Each row corresponds to a different gene, two rows for each gene, the first row corresponds to the replicate 1 and the second to the replicate 2.

first: Maria

middle: T

last: Lara Ortiz


title: Expression data from Xenopus laevis embryonic epidermis depleted for Jnk signalling

status: Public on Jun 24 2016

city: Richmond

first: Amanda

middle: J

last: Dickinson

state: Virginia

address: 1000 W Cary street

department: Biology

country: USA

institute: Virginia Commonwealth University

summary:
St. 14 embryos were incubated in 100mM of a Jnk inhibitor (SP600125)-0,1x MBS until stage 24. Embryonic epidermis was isolated and stored immediately in chilled (4°C) Trizol.  We sought to uncover all the putative targets of Jnk expresssed in the embryonic epidermis
whole embryonic skin was isolated and immediately stored in chilled trizol

overall_design: Xenopus embryos skins were isolated at stage 24 of early development for Trizol RNA extraction and hybridization on Affymetrix microarrays. Each sample contains 20 whole embryonic skins

first: Nathalie

last: HOUSSIN

last: DICKINSON

first: Stephen

last: TURNER


title: Loss of the DNA methyltransferase MET1 induces H3K9 hypermethylation at PcG target genes in Arabidopsis, and relocation of H3K27 trimethylation to transposons [array]

status: Public on Jun 22 2016

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary:
Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences.  Recently, ectopic genic DNA methylation in the CHG context (where H is any base except G) has been observed in globally DNA hypomethylated mutants such as met1, but neither the nature of the hypermethylated loci nor the biological significance of this epigenetic phenomenon have been investigated.  Here, we generated high-resolution genome-wide maps of both H3K9m2 and H3K27m3 in wild type and met1 plants, which we integrated with transcriptional data, to explore the relationships between these two marks. We found that most of the ectopic H3K9m2 observed in met1 is not due to defects in IBM1-mediated H3K9m2 demethylation, but instead targets H3K27m3-marked genes suggesting an interplay between these two silencing marks. Furthermore, H3K9m2/DNA-hypermethylation at these PcG targets in met1 is coupled with a decrease in H3K27m3 marks, whearas H3K9m2 hypomethylated transposons become ectopically H3K27me3 hypermethylated.  Our results bear interesting similarities with cancer cells, which show global losses of DNA methylation, but ectopic hypermethylation of genes previously marked by H3K27m3.

Keywords: Genome binding/occupancy profiling by genome tiling array

overall_design:
We used the met1-3 allele (Saze et al. 2003) and the salk_006042 line for isolating ibm1 mutants. met1-1st generation homozygous mutants and ibm1-1st generation homozygous mutants were isolated from a segragating population by genotyping. met1-2nd generation second mutants are the progeny of a single met1-1st generation homozygous mutant that was partially fertile. The entire shoots of 3 weeks old Arabidopsis plants (Col-0 ecotype), grown for 3 weeks under continuous light, were harvested, cross-linked as described in (Bernatavichute et al., 2007), frozen under liquid nitrogen and grown to powder (2g). Arabidopsis chromatin enriched for H3K9m2 and H3K27m3 was immunoprecipitated using an antibody that specifically recognizes H3K9m2 (Abcam 1220) and an antibody that specifically recognizes H3K27m3 (Upstate  07-449) respectively.  Unmodified H3 was immunoprecipitated using Abcam 1791-100.  Nucleosomal DNA and Input DNA were used as controls. ChIP, DNA purification and amplification were performed as in (Bernatavichute et al., 2007); Roche Nimblegen performed labelling and hybridization of the samples, washing and scanning resolution. All ChIP signals were normalized with either H3 ChIP or input genomic DNA by taking the log2 ratio and adjusted so that the average log2 ratio score across the genome was zero.
6 samples
Processed data can be downloaded at http://danio.pellegrini.mcdb.ucla.edu/~hume/Deleris_PLoSGen2012_H3K9m2data.zip


title: Gene expression profiles associated with the positive impact of an early plant-based diet exposure on its future acceptance in rainbow trout

status: Public on Jun 23 2016

city: St Pee sur nivelle

first: Inge

last: Geurden

address: Quartier Ibarron

department: PHASE

country: France

institute: INRA

summary: Sustainable aquaculture, which entails proportional replacement of fish-based feed sources by plant-based ingredients, is impeded by the poor growth response frequently seen in fish fed high levels of plant ingredients. To evaluate the potential to improve, by means of early nutritional exposure, the growth of fish fed plant-based feed, rainbow trout swim-up fry were fed for 3 weeks either a plant-based diet (diet V, V-fish) or a diet containing fishmeal and fish oil as protein and fat source (diet M, M-fish). After this 3-week nutritional history period, all V- or M-fish received diet M for a 7-month intermediate growth phase. Both groups were then challenged by feeding diet V for 25 days during which voluntary feed intake, growth, and nutrient utilization were monitored (V-challenge). The results of the V-challenge showed a  higher growth rate and higher feed intake in fish of nutritional history V compared to M (see PMID:24386155). To identify the molecular mechanisms that govern the enhancement of feed acceptance following early-feed exposure of diet V, we performed microarray expression analysis using swim-up fry collected at the end of early-feeding exposure (diet M and diet V), as well as brain and liver of juveniles sampled at the end of the V-challenge (M-his and V-his), and employing a rainbow trout microarray platform with 8 X 60K probes per slide. Persistently differentially expressed genes were identified by isolating probes that were differentially expressed (fold change ≥ 1.5 and p {nutritional history} ≤ 0.05), both at the end of the early exposure, and in either brain or liver of juvenile trout at the end of the V-challenge. Overall, 1787 (3-week + Brain) and 924 (3-week + Liver) mRNA probes were found to be persistently affected by nutritional history of early-feeding exposure. This positive response is encouraging as a potential strategy to improve the use of plant-based feed in fish, of interest in the field of fish farming and animal nutrition in general. Furthermore, the genes associated with mediating this positive early feeding effect, could serve as potential biomarkers to evaluate increasing acceptability of plant-based diets in fish farming.

overall_design: To identify potential genes associated with the positive impact of an early-feeding exposure of a plant-based diet on its future acceptance and utilization in rainbow trout, we employed microarray expression analysis on trout swim-up fry exposed to fish-based diet M (4 samples) or plant-based diet V (3 samples) for 3 weeks; and brain and liver of of juvenile trout with nutritional history of diet M (4 samples each) or diet V (4 samples each) after the 25 day V-challenge with plant based-diet.

first: Mukundh

middle: N

last: Balasubramanian

first: Stephane

last: Panserat

first: Mathilde

last: Dupont-Nivet

first: Edwige

last: Quillet

first: Francoise

last: Medale

first: Jerome

last: Montfort

first: Aurelie

last: Le Cam

first: Sadasivam

last: Kaushik


title: The miRNAs diversity between pancreatic body/tail and head cancers

status: Public on Jun 18 2016

city: Hangzhou

first: Qi

last: Ling

state: Zhejiang

address: 79 Qingchun road

department: Suegery

country: China

institute: Zhejiang University

summary: We aim to found the differentially expressed miRNAs between the two subtypes of pancreatic cancer

overall_design: Four paired (age, gender, CA-19-9, differentiation) pancreatic body/tail and head cancer tissues were used for a  Agilent Human miRNA Microarray Kit (8×15k), version 14.0 (design ID: 31945)

first: Holger

last: Kalthoff


title: Comparison of hatched blastocyst derived from IVV, PA,and CT

status: Public on Jun 19 2016

city: Madison

first: chi

last: zhou

state: WI

address: 202 S. Park Street, PAB1, Meriter Hospital

department: Department of OB/Gyn

institute: University of Wisconsin-Madison

summary: Comparative transcriptomic analyses among in vivo (IVV) HB, parthenogenetic activation (PA) HB, and chromatin transfer (CT) HB were performed following a reference design.

overall_design: Total RNA samples extracted from pools of 5 embryos were amplified, labelled with Cy5 dye and hybridized with Cy3 dye labelled reference RNA pool on EMPV1 [GPL14925] microarray following a reference design. Three biological replicates from each group were included in the comparative microarray analysis.

first: Chi

last: Zhou


title: Gene expression profile changes during blastocysts hatching of embryos produced from parthenogenesis and in vivo

summary: Comparative transcriptomic analyses among in vivo (IVV) XB, in vivo (IVV) HB, parthenogenetic activation (PA) XB, and parthenogenetic activation (PA) HB were performed following a reference design.


title: circRNA expression in cutaneous squamous cell carcinoma (cSCC)

city: Bochum

first: Michael

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

country: Germany

institute: Ruhr-University Bochum

summary:
Punch biopsies from patients with cSCC (n=3) and non-lesional skin (n=3) were included in the study. Microarray based circRNA expression profiles were acquired using Arraystar circRNA Arrays V. 2.0 screening for 13.617 distinct human circRNA candidates.
We identified circRNAs differentially expressed in cSCC compared to non-lesional skin (control).

overall_design: The circRNA expression in cSCC was compared to circRNA expression in non-lesional skin (control).


title: Gene expression profile changes during blastocysts hatching of embryos

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

overall_design: Refer to individual Series


title: Human whole blood samples: disease discordant twins and healthy controls.

status: Public on Jun 20 2016

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: We sought to utilize disease discordant twins and a novel viral-human gene microarray assay using whole human genome microarray in combination with a set of over 6,000 probes, which correspond to the majority of known viral genesrole of shared viral infections and the activation of shared antiviral signaling pathways in the development of SAID

overall_design: One-condition experiment, probands vs. unaffected twins vs healthy controls. Microarray replicates: two replicates for each gene probe

first: Lu

last: Gan

first: Zhennan

last: Lai


title: Exploiting microRNA and mRNA profiles generated in vitro from carcinogen-exposed primary mouse hepatocytes for predicting in vivo genotoxicity and carcinogenicity (mRNA)

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

summary: The well-defined battery of in vitro systems applied within chemical cancer risk assessment is often characterised by a high false-positive rate, thus repeatedly failing to correctly predict the in vivo genotoxic and carcinogenic properties of test compounds. Toxicogenomics, i.e. mRNA-profiling, has been proven successful in improving the prediction of genotoxicity in vivo and the understanding of underlying mechanisms. Recently, microRNAs have been discovered as post-transcriptional regulators of mRNAs. It is thus hypothesised that using microRNA response-patterns may further improve current prediction methods. This study aimed at predicting genotoxicity and non-genotoxic carcinogenicity in vivo, by comparing microRNA- and mRNA-based profiles, using a frequently applied in vitro liver model and exposing this to a range of well-chosen prototypical carcinogens. Primary mouse hepatocytes (PMH) were treated for 24 and 48h with 21 chemical compounds [genotoxins (GTX) vs. non-genotoxins (NGTX) and non-genotoxic carcinogens (NGTX-C) versus non-carcinogens (NC)]. MicroRNA and mRNA expression changes were analysed by means of Exiqon and Affymetrix microarray-platforms, respectively. Classification was performed by using Prediction Analysis for Microarrays (PAM). Compounds were randomly assigned to training and validation sets (repeated 10 times). Before prediction analysis, pre-selection of microRNAs and mRNAs was performed by using a leave-one-out t-test. No microRNAs could be identified that accurately predicted genotoxicity or non-genotoxic carcinogenicity in vivo. However, mRNAs could be detected which appeared reliable in predicting genotoxicity in vivo after 24h (7 genes) and 48h (2 genes) of exposure (accuracy: 90% and 93%, sensitivity: 65% and 75%, specificity: 100% and 100%). Tributylinoxide and para-Cresidine were misclassified. Also, mRNAs were identified capable of classifying NGTX-C after 24h (5 genes) as well as after 48h (3 genes) of treatment (accuracy: 78% and 88%, sensitivity: 83% and 83%, specificity: 75% and 93%). Wy-14,643, phenobarbital and ampicillin trihydrate were misclassified. We conclude that genotoxicity and non-genotoxic carcinogenicity probably cannot be accurately predicted based on microRNA profiles. Overall, transcript-based prediction analyses appeared to clearly outperform microRNA-based analyses.

overall_design: The study investigated differential gene expression in primary mouse hepatocyte mRNA following 24 and 48 hours of exposure to di(2-ethylhexyl)phthalate(DEHP), 4-Acetylaminofluorene(4AAF), Curcumin(Cur), Phenobarbital(PhB), Reserpine(Res), 7,12-Dimethylbenzanthracene (DMBA), Resorcinol(Resorcinol), Para-cresidine(pCres), Phenacetin(Phen), Diclofenac(diclo), Wy 14643(Wy), Tributyltinoxide(TBTO), Benzo[a]pyrene(BaP), 8-Hydroxyquinoline [AKA 8-quinolinol](8HQ), 17-b-estradiol(E2), ampicillin(AmpC), cisplatin(CisPl), Aflatoxin B1(AFB1), Cyclosporin A(CsA), 2,3,7,8-Tetrachlorodibenzo-p-dioxin(TCDD), Quercetin(Que) or their responsive solvent (dimethylsulfoxide(DMSO), Ethanol(ETOH), phosphate buffered saline(PBS)). Three biological replicates per compound/solvent. In total 184 arrays.

first: L


title: Copy number variation between BJ cells and BJ-derived iPS cells

city: Seattle

first: Takafumi

last: Hiramoto

address: 1959 NE Pacific Street, HSB K-260

department: Division of Hematology

institute: University of Washington

type: Genome variation profiling by genome tiling array

summary: Copy number variation analysis between BJ cells and BJ cells derived iPS cells which were established by using non-transmissible measles virus vector

overall_design: DNA derived from BJ cell and iPS cells were extracted and analysis using CGH array

first: Kenzaburo

last: Tani


title: A novel insulin receptor-binding protein enhances glucose uptake and glucose clearance in vitro and in vivo through triggering insulin receptor signaling pathway

status: Public on Jun 25 2016

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: In this study, a novel IR-binding protein (IRBP) from Momordica charantia, named as mcIRBP, was identified by analyzing the physical and functional interactions between mcIRBP and IR. The hypoglycemic effect and mechanism of mcIRBP were further evaluated in normal and streptozotocin-induced diabetic mice.

overall_design: Normal and diabetic mice were treated without or with mcIRBP and RNAs from muscle tissues were extracted for microarray analysis. Number of replicate was three.

first: Hsin-Yi

last: Lo

first: Chia-Cheng

last: Li

first: Tin-Yun

last: Ho


title: MicroRNA-674-5p/5-LO axis is important in concanavalin A-induced acute mouse liver injury

status: Public on Jun 27 2016

first: Kunkai

last: Su

address: 79 Qingchun Road

summary:
Eight-week-old male pathogen-free BALB/c mice were used for the induction of concanavalin A (Con A)-induced hepatitis. Animals were acclimated for at least 6-7 days to a 12-hour light/dark cycle in a humidity- and temperature-controlled, specific-pathogen-free environment in autoclaved cages. Mice were randomly assigned to two groups (4 in each group) and received Con A type IV (or saline) intravenously via the tail vein at the dose of 20 mg/kg for 2 hours. The animals were sacrificed for blood and liver collection. Blood was taken for transaminase and cytokine measurements. Livers were excised immediately after sacrifice. Part of the livers were immediately snap-frozen in liquid nitrogen and kept at -80°C for total RNA isolation and microRNA microarray analysis.
miR-674-5p and other miRNAs were experimentally validated to be dysregulated by Con A in mouse livers.

overall_design: Liver samples from four mice treated with Con A and four mice treated with saline were used to acquire the miRNA expression profiling.

last: Wang

first: Xin

last: Huang

first: Luoyang

last: Qi

first: Dasong

last: Hua

first: Jingjing

last: Tao

first: Bowen

last: Wu

first: Lijun

last: Ge

first: Danyan

last: Zhu

first: Yihan

last: Zhang

first: Yifan

first: Yijia

last: Lou

first: Lanjuan


title: Exploiting microRNA and mRNA profiles generated in vitro from carcinogen-exposed primary mouse hepatocytes for predicting in vivo genotoxicity and carcinogenicity (miRNA)

first: Linda

last: Rieswijk

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The study investigated differential gene expression in primary mouse hepatocyte mRNA following 24 and 48 hours of exposure to di(2-ethylhexyl)phthalate(DEHP), 4-Acetylaminofluorene(4AAF), Curcumin(Cur), Phenobarbital(PhB),Reserpine(Res), 7,12-Dimethylbenzanthracene (DMBA), Resorcinol(Resorcinol), Para-cresidine(pCres), Phenacetin(Phen), Diclofenac(diclo),Wy 14643(Wy), Tributyltinoxide(TBTO), Benzo[a]pyrene(BaP), 8-Hydroxyquinoline [AKA 8-quinolinol](8HQ), 17-b-estradiol(E2), ampicillin(AmpC), cisplatin(CisPl), Aflatoxin B1(AFB1), Cyclosporin A(CsA), 2,3,7,8-Tetrachlorodibenzo-p-dioxin(TCDD), Quercetin(Que) or their responsive solvent (dimethylsulfoxide(DMSO), Ethanol(ETOH), phosphate buffered saline(PBS)). Three biological replicates per compound/solvent. In total 184 arrays.

first: L


title: Sex-biased expression of miRNAs by microarray in critically endangered Amur sturgeon

status: Public on Jun 30 2016

city: Guangzhou City

first: Zhang

last: Xiujuan

state: Guangdong Province

address: 105 Xingang West Road, Haizhu District

institute: Guangdong Entomological Institute

summary: In this study, we utilized the microfluidics chip technology on the gonads of Amur sturgeon to identifiy gender-specific miRNAs. The probes of all miRNAs about 663 published in fish and our novel miRNAs from sturgeon were chosed in the microarray experiment.

overall_design: Above 4µg to 8µg total RNA from one female and one male separativley were performed the miRNA microarray assays.Each probe was repeated five times on the chip to ensure reproducibility of microarray.

first: Xiujuan

first: Jinping

last: Chen


title: Transcriptome analysis of wild type and erythromycin-producing strain of S. erythraea

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: Erythromycin is a medically important antibiotic, biosynthesized by the actinomycete Saccharopolyspora erythraea. We used transcriptomic approach to compare whole genome expression in erythromycin high-producing strain, compared to the wild type S. erythraea strain in four stages of fermentation.

overall_design: 2 strains (3 individual fermentations each), 4 time points --> 24 samples (2 exluded from anaysis, 22 remaining); one color design

first: Marko

last: Petek


title: To find out different expression lncRNAs between glioblastoma cancer and adjacent normal glioblastoma tissue

status: Public on Jun 21 2016

city: Shanghai

first: Weijie

last: Min

state: Yangpu

address: Changhai road NO.168

department: Neurosurgery

institute: Changhai Hospital,Second Military Medical University

summary: To further understand the molecular mechanisms in the development of glioblastoma cancer, we employed this microarray to identify lncRNAs associated with glioblastoma cancer.

overall_design: 4 pairs of glioblastoma cancer tissues and normal glioblastoma tissues were collected after glioma operation.

first: Zhijian

last: Yue


title: Transcriptome analysis of LfeRT32a in its natural microbial community comparing the biofilm and planktonic modes of life

city: Torrejón de Ardoz

first: Mercedes

last: Moreno

state: Madrid

address: Crta. de Ajalvir, km 4

country: Spain

institute: Centro de Astrobiología

summary:
Full title: Environmental transcriptome analysis of LfeRT32a in its natural microbial community comparing the biofilm and planktonic modes of life.
Extreme acidic environments are characterized among other features by the high metal content and the lack of nutrients (oligotrophy). Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream attached to solid substrates (streamers). In the Tinto River (Spain), brown filaments develop under the water stream where the Gram-negative iron-oxidizing bacteria Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans are abundant.
Both microorganisms play a critical role in bioleaching processes for industrial (biominery) and environmental applications (acid mine drainage, bioremediation). The aim of this study was to investigate the physiological differences between the free living (planktonic) and the sessile (biofilm associated) lifestyles of L. ferrooxidans as part of a natural extremely acidophilic community.

overall_design: Differential expression profile of biofilm cells using planktonic cells as control. Two biological replicates. Two replicates per array.

last: Moreno-Paz

first: Manuel

last: Gómez

first: Aida

last: Arcas

first: Víctor

last: Parro


title: Somatically Acquired Structural Genetic Differences; a Longitudinal Study of Elderly Danish Twins

city: Odense C

first: Lene

last: Christiansen

address: J.B. Winsloews Vej 9B

department: Epidemiology, Biostatistics and Biodemography

country: Denmark

institute: University of Southern Denmark

summary: Structural genetic variants like copy number variants (CNVs) comprise a large part of human genetic variation and may be inherited as well as somatically acquired. Recent studies have reported the presence of somatically acquired structural variants in the human genome and it has been suggested that they may accumulate in elderly individuals. To further explore the presence and the age-related acquisition of somatic structural variants in the human genome, we investigated CNVs acquired over a period of 10 years in 86 elderly Danish twins as well as CNV discordances between co-twins of 18 monozygotic twin pairs. Furthermore, the presence of mosaic structural variants was explored.

overall_design:
86 elderly Danish twins from 18 monozygotic and 25 dizygotic twin pairs were sampled twice 10 years apart. After genotyping and calling of structural variants (both non-mosaic and mosaic), paired samples (i.e. samples from monozygotic twins or longitudinal samples from the same individual) were compared and structural variation differences were identified. Genotyping was performed on two different arrays (Illumina HumanOmniExpress and HumanOmni2.5M) but only the 716,299 overlapping SNPs were included in the analysis.

6 samples have no raw data due to server breakdown and data loss: GSM1985680, GSM1985684, GSM1985687, GSM1985703, GSM1985710, and GSM1985718

first: Kristina

middle: M

last: Koldby

first: Marianne

last: Nygaard

first: Kaare

last: Christensen


title: Mating and sperm-free seminal fluid changes the gene expression in the utero-vaginal junction of White Leghorn hens

city: Linköping

first: Mohammad

last: Atikuzzaman

address: Linköping

department: Clinical and Experimental Medicine

country: Sweden

institute: Linköping University

summary: Spermatozoa being foreign to the female are to be promptly eliminated after deposition by the local immune defense of female. However, avoiding the local immune defense sperm can be stored in the utero-vaginal junction for weeks and keep their fertilization ability. Whether, UVJ changes their gene expression after mating or SF-infusion to tolerate thjose forign cells are not understood. Therefore this study was done to observe the gene expression in the utero-vaginal junction after mating or SF-infusion.

overall_design: Twelve White Leghorn chicken were devided into three groups- either hens were kept without mating or insemination (control, n=4) or paired with a male chicken of the same breed (treatment 1, n=4) or inseminated with sperm-free seminal fluid (treatment 2, n=4). The utero-vaginal junction was removed 24 h after mating or insemination.

first: Heriberto

last: Rodriguez-Martinez


title: EventPointer: An effective identification of alternative splicing events using junction arrays

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

summary: There is an increasing interest on the role of Alternative splicing (AS) in different pathologies. The Affymetrix Human Transcriptome Array (HTA 2.0) can be used to explore AS very efficiently. However, the interpretation software provided by its vendor (TAC 3.0) does not fully exploit its potential and can only be applied to case-control studies.  EventPointer is an R package to identify Alternative Splicing events using HTA 2.0 arrays. It can be applied to complex experimental designs. The software provides a list of the detected events indicating the type of event (cassette, alternative 3’, etc.), their statistical significance, and affected protein domains affected. The false positive rate is very low (the first detected false positive was ranked in the 149th position). EventPointer is publicly available at GitHub.

overall_design: 9 samples with 3 replicates from A549 lung adenocarcinoma cell lines. The experiment includes 3 conditions: Cells treated with the transfection vehicle (Lipofectamine), cells treated with scrambled RNA and cells transfected with a siRNA that targets SRSF1

middle: P

first: Ander

last: Muniategui

first: Fernando

last: de Miguel

last: Aramburu

first: Luis

last: Montuenga

first: Ruben

last: Pio

first: Angel

last: Rubio


title: Nuclear receptor coactivator 1 (NCOA1) is involved in the regulation of PCa cell migration via PRKD1

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary: Due to the urgent need of new targeting strategies in PCa, AR interacting proteins should be considered. In this study we aimed to test the effect of a long-term knockdown of NCOA1, an AR coactivator, in PCa progression and metastatogenesis and whether NCOA1 could be used as a possible therapeutic target. To test the consequences of NCOA1 knockdown on proliferation, we performed by 3H thymidine incorporation assays revealing a strong reduction in castration resistant MDA PCa 2b and androgen-dependent LNCaP cells, without affecting AR negative PC3 cells. Furthermore, Boyden chamber assays revealed a strong decrease in migration and invasion upon NCOA1 knockdown. Using a cDNA microarray, we identified protein kinase D1 (PRKD1) as one prominent upregulated gene in MDA PCa 2b, which was not seen in PC3 cells. Knockdown of PRKD1 clearly reverted the reduced migratory potential. Moreover, we found phospholipase A2, group7 (PLA2G7) and eukaryotic translation initiation factor 5A2 (EIF5A2), which might be involved in migration of PC3 cells. Further, we can clearly demonstrate that PRKD1 is negatively regulated by the AR/NCOA1 complex. In addition, immunhistochemical staining revealed a strong increase in NCOA1 expression in matched and unmatched patients’ samples, respectively between normal prostate and primary tumor. Regarding the PRKD1 staining, no final conclusion can be drawn in terms of a tumor suppressor function. Thus, our findings directly associate NCOA1/AR complex with PRKD1 regulation and further suggest NCOA1 as a potential therapeutic target also due to the effect on PC3 cell migration.

overall_design: Cell lines with a stable knockdown of NCOA1 were generated by lentiviral-based transduction of shRNA vectors. For each of the two cell lines MDA and PC3, gene expression profiles were generated for KO and CTRL samples with 3 biological replicates for each. Differential expression analysis was performed by comparing the gene expression estimates between KO and CTRL samples for each cell line.

first: Birgit

last: Luef

first: Florian

last: Handle

first: Gvantsa

last: Kharaishvilli

first: Martina

last: Hager

first: Günter

last: Janetschek

first: Stefan

last: Hruby

first: Christine

last: Englberger

first: Jan

last: Bouchal

first: Frederic

middle: R

last: Santer

first: Zoran

last: Culig


title: Gene expression changes in response to carmustine treatment in glioma cells with acquired carmustine resistance versus parent cell lines

city: Silver Spring

first: Salaheldin

middle: Sobhi

last: Hamed

state: Maryland

address: 10903 New Hampshire Ave

department: CDER/OTR

institute: U.S. FDA

summary: Three glioma cell lines (A172CR, SW1088CR, and U87CR) developed resistance to carmustine by prolonged sublethal exposure to 11 cycles of increasing carmustine exposure. The gene expression of parent versus resistant cell lines was compared upon exposure to carmustine. DMSO (vehicle) treatment was used as a control.

overall_design: After 1 hour of exposure to either carmustine or DMSO, the gene expression profile of resistant versus parent cell lines was quantified. Indirect pairwise comparison between resistant versus parent cell line upon exposure to either carmustine or DMSO was performed in pair of dye swap experiments.

middle: S

first: Charles

last: Roth


title: Comparative transcriptomic analysis of an evolved and an ancestral  wine yeast strains presenting differences in the bioconversion of higher alcohols to acetate esters

status: Public on Jun 29 2016

city: MONTPELLIER

first: Sylvie

last: Dequin

address: 2 PLACE PIERRE VIALA

institute: INRA

summary: An evolved strain (ECA5) presented two successive yields of bioconversion of higher alcohols to acetate esters, while its parental strain (EC1118) had a constant yield through the fermentation. Transcriptomic analysis was performed during wine fermentation in SM330 containing 8mg/L phytosterols, at  35 g/l and at 70 g/l of CO2 released. For ECA5, this corresponds to a sample before and one after the change of bioconversion yield. This analysis helped us to understand the different management of lipid source by the evolved strain, which is probably linked to a greater availability in acetyl-CoA.

overall_design: Two strains (EC1118 and ECA5) were compared during wine fermentation at 2 released CO2 time point (35g/L and 70g/L). Each condition is in triplicat.

first: Stéphanie

last: Rollero

first: Jean-Roch

last: Mouret

first: Isabelle

last: Sanchez

first: Carole

last: Camarasa

first: Jean-Marie

last: Sablayrolles


title: Evaluation of autoantibody signatures in meningioma patients using human proteome array

city: Mumbai

first: Sanjeeva

last: Srivastava

address: Powai

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Bombay

summary:
Our objective was to identify the potential autoantibody markers in meningiomas using high-density human proteome arrays (~17,000 full-length recombinant human proteins).
This study revealed the dysregulation of 489 and 104 proteins in grades I and II of meningioma, respectively, along with the enrichment of signalling pathways which play a major role in the manifestation of the disease. This study revealed the dysregulation of 489 and 104 proteins in grades I and II of meningioma, respectively, along with the enrichment of signalling pathways which play a major role in the manifestation of the disease. Autoantibody targets like IGHG4, CRYM, EFCAB2, STAT6, HDAC7A and CCNB1 were dysregulated across both grades.

overall_design: We performed screening of sera from 15 healthy controls, 10 Grade I and 5 Grade II meningioma patients.

first: Parvez

last: Syed

first: Shabarni

last: Gupta

first: Shuvolina

last: Mukherjee

first: Narendra

middle: G

last: Pandala

first: Saket

last: Choudhary

first: Heng

last: Zhu

first: Sridhar

last: Epari

first: Santosh

last: Noronha

first: Aliasgar

last: Moiyadi


title: Exploiting microRNA and mRNA profiles generated in vitro from carcinogen-exposed primary mouse hepatocytes for predicting in vivo genotoxicity and carcinogenicity

first: Linda

last: Rieswijk

type:
Expression profiling by array
Non-coding RNA profiling by array

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

overall_design: Refer to individual Series


title: The impact of manganese on biofilm development of Bacillus subtilis.

city: Jena

first: Akos

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

summary: Transcriptome comparison of Bacillus subtilis 168 grown on solid agar (sample 1-3) or aerated liquid (sample 4-7) 2xSG medium with and without of 0.1 mM manganese.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: B subtilis 168 wild type cells were grown on the top of 2xSG solid medium with 1.5% agar concentration (samples 1-3) with and without manganese in the medium. B subtilis 168 wild type cells were grown in aerated (225rpm) 2xSG liquid medium (samples 4-7) with and without manganese in the medium. In the first experiments 3 biological replicates, while in the second one, 4 biological replicates were used. Dye swaps are included in both experiments.

first: Eisha

last: Mhatre


title: Perturbation of epigenetic processes by doxorubicin in the mouse testes: microRNA analysis

city: Didcot

first: Emma

middle: Louise

last: Marczylo

state: Oxfordshire

address: Harwell Campus, Chilton

department: Toxicology

country: United Kingdom

institute: Public Health England

summary: microRNA profiling of mouse testis comparing treatment with doxorubicin to vehicle only control (published in Toxicology Research, DOI: 10.1039/C6TX00078A)

overall_design: Two-condition experiment, doxorubicin vs control at 3 time points (1wk, 4wk and 7 wk following treatment). Biological replicates: 12 control, 12 doxorubicin (implementing a dye swap design of n=6 forward and n=6 reverse). One replicate per dual colour array (total of 36 arrays).

middle: L


title: Copy number variation data in malignant mouse mammary cell lines

status: Public on Jun 15 2016

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

summary: Many preclinical therapy studies have focused on a small number of well-described mouse allograft or human xenograft models that poorly represent the heterogeneity of human disease.  Here we have assembled a panel of mouse mammary cell lines derived from spontaneously-arising mouse mammary tumors or from mammary tumors arising in genetically engineered mouse models.  We used the Affymetrix Mouse Diversity Genotyping Array to address DNA copy number variation in the genomes of the cell lines of this panel.  The resulting information about regions of amplification and deletion should help inform biological analyses as well as provide a reference for cell line authentication/identification.

overall_design: Affymetrix Mouse Diversity Genotyping arrays were used according to manufacturer's directions to analyze  gDNA extracted from 27 mouse mammary cell lines of varying malignancy.

first: Lalage

last: Wakefield

first: Kent

last: Hunter

first: Jeffrey

last: Green

first: Yu-an

last: Yang


title: Acquired resistance of Jurkat cells to TNF-related apoptosis-inducing ligand (TRAIL)

city: Basel

first: Robert

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has been shown to be a potent inducer of apoptosis in various cancer cell lines and primary cancer cells. However, in clinical trials administration of recombinant TRAIL or TRAIL death receptor agonists did not show sufficient efficacy for treatment of tested malignant disorders compared to standard chemotherapy. Acquired resistance of cancer cells to TRAIL and to other “death receptor” ligands may explain not only the inability of TRAIL and TRAIL “death receptor” agonists to achieve the clearance of cancer cells in vivo but also the escape of cancer cells from immune cell – mediated killing. Selective pressure of TRAIL on TRAIL-sensitive Jurkat T-lymphoblastic leukemia cells provided several TRAIL resistant Jurkat cell line clones (TR1, TR2, TR3). We showed that acquired TRAIL resistance was associated with complex disruption of both extrinsic and intrinsic apoptotic pathways manifested by acquired multi-drug resistant phenotype of TR1, TR2, and TR3 clones. To identify changes associated with TRAIL resistance of Jurkat cells we performed genome-wide gene expression analysis of TRAIL-resistant clones (TR) and compared to WT Jurkat cells. We identified significantly increased expression (1.33-fold change with adjusted p < 0.05) of 73 genes in TR1 clone, 53 genes in TR2 clone and 8 genes in TR3 clone, and significant decrease in expression (0.75-fold change with adjusted p < 0.05) of  174 genes in TR1 clone, 36 genes in TR2 clone and 28 genes in TR3 clone. There was an overlap of only 2 significantly overexpressed (midkine / MDK and zinc finger and BTB domain containing 16 gene / ZBTB16 / PLZF)   and 4 downregulated genes (YAP1, IGJ, EIF1AY, RPS4Y1) in all three TR clones.

overall_design: Total cellular RNA was isolated from biologic duplicates of untreated Jurkat cells (WT) and TRAIL resistant Jurkat cell line subclones (TR1, TR2, TR3) established by selective pressure of TRAIL 1000 ng/mL on Jurkat cells over the period of 12 weeks.

first: Pavel

last: Klener

first: Jan

last: Zivny


title: Metagenomic analysis revealed higher microbial and functional gene diversities in deep landfill

city: Beijing

first: Mengjing

last: Xia

address: No.5 Yiheyuan Road

institute: Peking University

summary: Waste decomposition in landfills is a complex and microbe-mediated process. Understanding the microbial community composition and structure is critical for accelerating decomposition and reducing adverse impact on the environment. Here, we examined the microbial communities along with landfill depth and age (LDA) in a sanitary landfill in Beijing, China using 16s rRNA Illumina sequencing and GeoChip 4.6. We found that Clostridiales and Methanofollis were the predominant bacteria and archaea in the present landfill, respectively. Interestingly, in contrast with the decreasing trend of microbial diversity in soil, both phylogenetic and functional diversities were higher in deeper and older refuse in the landfill. Phylogenetic compositions were obviously different in the refuse with the same LDA and such difference is mainly attributed to the heterogeneity of refuse instead of random process. Nevertheless, functional structures were similar within the same LDA, indicating that microbial community assembly in the landfill may be better reflected by functional genes rather than phylogenetic identity. Mantel test and canonical correspondence analysis suggested that environmental variables had significant impacts on both phylogenetic composition and functional structure. Higher stress genes, genes for degrading toxic substances and endemic genes in deeper and older refuse indicated that they were needed for the microorganisms to survive in the more severe environments. This study suggests that landfills are a repository of stress-resistant and contaminant-degrading microorganisms, which can be used for accelerating landfill stabilization and enhancing in situ degradation.

overall_design: Fifteen refuse samples with five landfill depths and ages (6m/2a, 12m/4a, 18m/6a, 24m/8a and 30m/10a) were collected from a sanitary landfill in Beijing, China. Three replicates in every landfill depth and age

first: Zhenshan

last: Li


title: Acquired resistance of Jurkat cells to TNF-related apoptosis-inducing ligand (TRAIL): a role for histone deacetylase inhibitors as powerful apoptosis sensitizer.

summary: Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has been shown to be a potent inducer of apoptosis in various cancer cell lines and primary cancer cells. However, in clinical trials administration of recombinant TRAIL or TRAIL death receptor agonists did not show sufficient efficacy for treatment of tested malignant disorders compared to standard chemotherapy. Acquired resistance of cancer cells to TRAIL and to other “death receptor” ligands may explain not only the inability of TRAIL and TRAIL “death receptor” agonists to achieve the clearance of cancer cells in vivo but also the escape of cancer cells from immune cell – mediated killing. Selective pressure of TRAIL on TRAIL-sensitive Jurkat T-lymphoblastic leukemia cells provided several TRAIL resistant Jurkat cell line clones (TR1, TR2, TR3). Irrespective of molecular changes histone deacetylase inhibitors (HDACi), such as suberoylanilide-hydroxamic acid (SAHA, vorinostat), were able to restore sensitivity of all three TRAIL-resistant clones to TRAIL. Gene expression analysis of TR1 clone treated with SAHA 1microM for 12 hours compared to untreated TR1 clone showed significant decrease in expression of CFLAR/cFLIP (0.71; p=0.006), BIRC5/survivin (0.80; p=0.024) and BID (0.66; p<0.001). Expression of both TRAIL “death” receptors DR4 (1.57; p<0.001) and DR5 (1.47; p=0.002) were significantly increased compared to untreated TR1 cells. The mRNA expression of caspases-2,-3,-8,-9,-10 did not significantly change with the SAHA treatment.

overall_design: Total cellular RNA was isolated from biologic duplicates of untreated Jurkat cells (WT), TRAIL resistant Jurkat cell clone (TR1) and  1 µM and 0.5 µM suberoylanilide-hydroxamic acid (SAHA, vorinostat) treated TR1 cell clones for 12 hours. Jurkat cell line subclones TR1was established by selective pressure of TRAIL 1000 ng/mL on Jurkat cells over the period of 12 weeks.


title: Photorespiratory stress  low CO2 conditions

status: Public on Jun 10 2016

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

summary: Six weeks old Arabidopsis plants were transferred to a low CO2 (100 ppm) environment during 24 hours and compared to control plants kept under ambient CO2 conditions. Limited CO2 availability will cause higher rates of photorespiration and affect the plant redox homeostasis. We studied the transcriptomic impact of exposing plants to a lower CO2 environment to further eliculidate the signaling pathways during photorespiratory stress.

overall_design: After 6 weeks plants were transferred to low CO2 conditions (100 ppm) during 24 h or kept at 400 ppm CO2 (control condition). Design: 3 replicates x 2 conditions (low CO2 - ambient CO2)

first: Frank

last: Van Breusegem


title: FIRST PHASE I TRIALS OF SLEEPING BEAUTY-MODIFIED CD19-SPECIFIC T CELLS

status: Public on Jun 08 2016

city: houston

first: sourindra

last: maiti

state: texas

address: 7455 Fannin Street

department: Pediatrics

institute: M.D. Anderson Cancer Center

summary: Background: T cells expressing antigen-specific chimeric antigen receptors (CARs) improve outcomes for CD19-expressing B-cell malignancies. We provide the first human application of T cells genetically modified using the Sleeping Beauty (SB) transposon/transposase system to express a CD19-specific CAR.  Methods: T cells were genetically modified using DNA plasmids from the SB platform to stably express a second-generation CD19-specific CAR and selectively propagated ex vivo with activating and propagating cells (AaPC) and cytokines. Twenty-six patients with advanced NHL and ALL safely underwent hematopoietic stem-cell transplantation (HSCT) and infusion of CAR T cells as adjuvant therapy in the autologous (n=7) or allogeneic settings (n=19).  Results: SB-mediated genetic transposition and stimulation resulted in 2,200-2,500-fold ex vivo genetically modified T-cell expansion, with 84% CAR expression, and without integration hotspots. The 30-month progression-free and overall survivals were 83% and 100%, respectively, following autologous HSCT, and the respective 12-month rates after allogeneic HSCT were 53% and 63%. No acute or late toxicities and no exacerbation of graft-versus-host-disease were observed. Despite a low antigen burden and unsupportive recipient cytokine environment, CAR T cells persisted for an average of 201 days for autologous and 51 days for allogeneic recipients.  Conclusions: CD19-specific CAR T cells generated with SB and AaPC platforms were safe, and may provide additional cancer control as planned infusions after HSCT, supporting further clinical development of this non-viral gene therapy approach.

overall_design: Total RNA obtained from Unmanipulated quiescent CD3+ T cells and ex vivo expanded CD19CAR+ day 28 T cells

first: Partow

last: Kebriaei

first: Harjeet

last: Singh

first: M

middle: H

last: Huls

first: Matthew

last: Figliola

first: Roland

last: Bassett

first: Simon

last: Olivares

first: Sonny

last: Ang

first: Margaret

last: Dawson

first: Pappanaicken

last: Kumaresan

first: Shihuang

last: Su

first: Sourindra

last: Maiti

first: Jianliang

last: Dai

first: Branden

last: Moriarity

first: Marie-Andrée

last: Forget

first: Vladimir

last: Senyukov

first: Aaron

last: Orozco

first: Tingting

last: Liu

first: Jessica

last: McCarty

first: Rineka

last: Jackson

first: Judy

last: Moyes

first: Gabriela

last: Rondon

first: Muzaffar

last: Qazilbash

first: Stefan

last: Ciurea

first: Amin

last: Alousi

first: Yago

last: Nieto

first: Katy

last: Rezvani

first: David

last: Marin

first: Uday

last: Popat

first: Chitra

last: Hosing

first: Elizabeth

last: Shpall

first: Hagop

last: Kantarjian

first: Michael

last: Keating

first: William

last: Wierda

first: Kim

middle: A

last: Do

last: Largaespada

first: Dean

first: Perry

middle: B

last: Hackett

first: Richard

middle: E

last: Champlin

first: Laurence

last: Cooper


title: Shewanella piezotolerans WP3 wild-type strain heat shock for 90 min

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: The WP3 strains was cultured at 20°C and heat shocked at 40°C for 90 min. The transcriptional profiles after and before heat shock were compared.

overall_design: Three biological replicates sample and 6 technical replicates for each experiment

first: Shengkang

last: Li

first: Fengping

last: Wang


title: A sunflower WRKY transcription factor stimulates the mobilization of seed-stored reserves during germination and post-germination growth

status: Public on Jun 04 2016

city: Santa Fe

first: Karina

last: Ribichich

state: Santa Fe

address: Colectora Ruta Nac. Nº168 km. 0

country: Argentina

institute: IAL

summary: Germinating oilseeds convert stored lipids into sugars and thereafter in metabolic energy that is used in seedling growth and establishment. During germination, the induced lipolysis linked to the glyoxylate pathway and gluconeogenesis produces sucrose, which is then transported to the embryo and driven through catabolic routes. Herein, we report that the sunflower transcription factor HaWRKY10 regulates carbon partitioning by reducing carbohydrate catabolism and increasing lipolysis and gluconeogenesis. HaWRKY10 was regulated by abscisic acid and gibberellins in the embryo leaves and highly expressed during sunflower seed germination and seedling growth, concomitantly with lipid mobilization. Sunflower leaf discs overexpressing HaWRKY10 showed repressed the expression of genes related to sucrose cleavage and glycolysis compared to controls. Moreover, HaWRKY10 constitutive expression in Arabidopsis seeds produced higher decrease in lipid reserves, whereas starch and sucrose were more preserved compared to wild type. Gene transcripts abundance and enzyme activities involved in stored lipid mobilization and gluconeogenesis increased more in transgenic than in wild type seeds 36 hours after imbibition whereas the negative regulator of lipid mobilization, ABI4, was repressed. Altogether, the results point out a functional parallelism between tissues and plant species, and reveal HaWRKY10 as a positive regulator of storage reserve mobilization in sunflower.

overall_design: Transient sunflower discs (Manavella and Chan, Nature Protocols 2009) 35S Promoter::GUS vs. 35S Promoter::HaHB11. Three biological replicates each.

first: J

last: Raineri

first: M

middle: D

last: Hartman

first: R

last: Chan

first: A

last: Iglesias

first: K

middle: F


title: In vitro infection of Bovine monocytes with Mycoplasma bovis delays apoptosis and suppresses production of IFNγ and TNF-α but not IL-10

status: Public on Jun 07 2016

city: Saskatoon

first: Erin

last: Scruten

state: Saskatchewan

address: 120 Veterinary Road

country: Canada

institute: VIDO-Intervac

summary: Mycoplasma bovis is one of the major causative pathogens of the bovine respiratory complex disease that is characterized by enzootic pneumonia, mastitis, pleuritis and polyarthritis.  M. bovis enters and colonizes the bovine respiratory epithelia through inhalation of aerosol from contaminated air.  The nature of the interaction between M. bovis and bovine innate immune system is not well understood.  We hypothesized that M. bovis invades blood monocytes and regulates cellular function to support its persistence and systemic dissemination.  We used bovine-specific peptide kinome arrays to identify cellular signaling pathways that could be relevant to M. bovis-monocyte interaction in vitro.  We validated these pathways using functional, protein and gene expression arrays.  Here we show that infection of blood monocytes with M. bovis delays spontaneous or TNF-α/staurosporine-driven apoptosis, activates NF-κβ p65 subunit and inhibits caspase-9 activity.  We also report that M. bovis infected bovine monocytes do not produce IFN-γ and TNF-α, although production of IL-10 is elevated.  Our findings suggest that M. bovis takes over the cellular machinery of bovine monocytes to prolong bacterial survival and to possibly facilitate subsequent systemic distribution.

overall_design: There were 6 samples analyzed.

first: Musa

last: Mulongo

first: Tracy

last: Prysliak

first: Scott

last: Napper

first: Jose

last: Perez-Casal


title: Expression data from lipopolysaccharide treated and untreated equine alveolar macrophages and basal comparison with peritoneal macrophages

status: Public on Jun 06 2016

city: Edinburgh

first: Anna

middle: Eleonora

last: Karagianni

address: Easter Bush Campus

institute: The Royal (Dick) School of Veterinary Studies and The Roslin Institute

summary:
Alveolar macrophages are the first line of defense against pathogens in the lungs of all mammalian species and therefore may constitute an appropriate therapeutic target cell in the treatment and prevention of opportunistic airway infections.  Analysis of alveolar macrophages from several species has revealed a unique cellular phenotype and transcriptome, presumably linked to their distinct airway environment and function in host defense.  The current study extends these findings to the horse.
Firstly, the transcriptome of equine alveolar macrophages was compared to that of equine peritoneal macrophages. This comparison revealed the differential basal expression of 451 genes. Gene expression analysis revealed an alternative macrophage polarisation profile in alveolar macrophages and a hybrid macrophage activation profile in peritoneal macrophages, a phenomenon potentially attributable to a degree endotoxin tolerance. Secondly, the change in gene expression profile of equine AMs following lipopolysaccharide stimulation was investigated. This revealed a significant change in the expression of 240 genes, including well known upregulated inflammatory genes.

overall_design: Equine untreated alveolar and peritoneal macrophages, as well as six hours lipopolysaccharide treated alveolar macrophages were used for RNA extraction and hybridization on Affymetrix microarrays.  We sought to characterise the specific biology of the equine alveolar macrophage, we analysed the basal gene expression of equine alveolar macrophages and made comparisons with (a) the basal gene expression of an alternative macrophage population (peritoneal macrophages) and (b) the LPS-induced gene expression of equine alveolar macrophages.

first: Ronan

last: Kapetanovic

first: Kim

last: Summers

first: Bruce

middle: C

last: McGorum

first: David

last: Hume

last: Pirie


title: Shewanella piezotolerans WP3 wild-type strain heat shock for 30 min

city: Shanghai

first: Huahua

last: Jian

summary: The WP3 strains was cultured at 20°C and heat shocked at 40°C for 30 min. The transcriptional profiles after and before heat shock were compared.

first: Shengkang

last: Li

first: Fengping

last: Wang


title: A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma [HumanHT-12 WG-DASL V4.0]

status: Public on Jun 01 2016

city: new delhi

first: binay

last: panda

address: 1649A vasant kunj

institute: ganit labs foundation

summary: Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of aggressive tumors in the head and neck region, with a rising incidence among younger population. The role of altered DNA methylation in OTSCC and its link with clinical parameters has not been fully assessed yet. We performed genome-wide methylation analysis of oral tongue primary tumors (n = 52)  using 485, 512 probes and correlated altered methylation with differences in gene expression. We used an ensemble machine-learning algorithm to identify differentially methylated probes and regions predictive of survival, risk habits, nodal status, tumor stage, and HPV infection followed by validation using data from the cancer genome atlas (TCGA) project on oral tongue (n = 24) and tumors from all subsites of head and neck region (n = 50).

overall_design: Whole-genome gene expression profiling was carried out with Illumina HumanHT12 v4 expression BeadChip (Illumina, San Diego, CA) with 21 tumors and their matched adjacent normal tissues. Total RNA was extracted using PureLink RNA mini kit (Invitrogen) and RNA quality was checked on the bioanalyzer using RNA Nano6000 chip (Agilent). RNA samples with poor RIN numbers (≤7) on the bioanalyzer chip, indicating partial degradation of RNA were processed using Illumina WGDASL assay and the ones with good RIN numbers (>7) were labelled using Illumina TotalPrep RNA Amplification kit (Ambion) as per the manufacturer’s recommendations. Targets were used to hybridize arrays and arrays were processed according to the manufacturer’s recommendations. Arrays were scanned using HiScan, Illumina, and the data collected were analyzed with GenomeStudio V2011.1 Gene Expression module 1.9.0 (Illumina) to check for the assay quality control probes. Raw signal intensities were exported from GenomeStudio for transformation, normalization and differential expression analyses using R.

first: Neeraja

middle: M

last: Krishnan

first: Kunal

last: Dhas

first: Jayalakshmi

last: Nair

first: Gangotri

last: Siddappa

first: Amritha

last: Suresh

first: Vikram

last: Kekatpure

first: Moni

last: Kuriakose

first: Binay

last: Panda


title: A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma [HumanHT-12 V4.0]


title: Transcriptional responses in Arabidopsis seedlings after hydrogen peroxide treatment

first: Patrick

last: Willems

summary: Excessive levels of reactive oxygen species (ROS) cause cellular stress through damage to all classes of macromolecules and result in cell death. However, ROS can also act as signaling molecules in various biological processes. In plants, ROS signaling has been documented in environmental stress perception, plant development and cell death amongst others. Knowledge on the regulatory events governing ROS signal transduction is however still scratching the surface. To further elucidate the transcriptional response and regulation upon ROS accumulation we supplemented Arabidopsis seedlings with a 10mM hydrogen peroxide (H2O2) solution to trigger oxidative stress.

overall_design: After growth of 7 days, hydrogen peroxide (H2O2) was added to a final concentration of 10mM. Control plants were treated with the same volume of H2O. Seedlings were grown for 24h under the same controlled conditions. Design: 3 replicates x 2 conditions (7+1 day H2O or 7+1 day H2O2)

first: Jordi

last: Denecker

first: Frank

last: Van Breusegem


title: Boxer dataset for genome-wide association study of modifiers of risk of canine degenerative myelopathy in dogs homozygous for SOD1 mutation

city: Cambridge

first: Kerstin

last: Lindblad-Toh

state: MA

address: 715 Main Street

department: Vertebrate Genome Biology

country: USA

institute: Broad Institute

summary: Degenerative myelopathy (DM) is a canine disease very similar to amyotrophic lateral sclerosis (ALS) in humans. We previously showed that DM is a promising model for ALS, as genome-wide association identified a mutation in SOD1, a known ALS gene. In this study, we identify a modifier gene, SP110, which strongly affects overall disease risk and age-of-onset in Pembroke Welsh corgis at risk of DM. Dissecting the complex genetics of this disease in a model organism may lead to new insights about risk and progression in both canine and human patients.

overall_design: 15 DM-affected and 10 unaffected Boxers homozygous for SOD1 mutation genotyped using the Illumina CanineHD array (~170,000 SNPs genomewide)

first: Emma

last: Ivansson

first: Katherine

middle: J

last: Megquier


title: Emergence of neural crest identity is a key early step in melanoma formation [Affymetrix]

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: The “cancerized field” concept posits that cells of a given tissue share a potentially oncogenic mutation or insult and are thus cancer-prone, yet only discreet clones within the field initiate tumor formation.  In melanoma, tumors frequently (~50%) carry the oncogenic BRAFV600E mutation that is also nearly always present in benign nevi that rarely become melanoma. The zebrafish crestin gene is expressed embryonically in neural crest progenitors and is then specifically re-expressed in melanoma tumors.  Here, we show by live imaging transgenic zebrafish crestin reporters that single melanocytes in a cancerized field with oncogenic BRAFV600E and p53 tumor suppressor loss undergo a change that recapitulates the neural crest progenitor (NCP) state, and patches of these cells initiate early melanoma. The crestin element is regulated by the NCP transcription factor sox10.  Forced sox10 overexpression in melanocytes accelerated melanoma formation, consistent with reprogramming to the NCP state and activation of super-enhancers that lead to melanoma. Our work highlights the importance of the reemergence of the NCP state as a barrier to melanoma initiation.

overall_design: Comparison of gene expression for single scales taken from melanoma-prone zebrafish of the p53/BRAF/Na/MiniCoopR/crestin:EGFP background with 3 crestin:EGFP (+) scales compared to 3 crestin:EGFP (-) scales.

first: Charles

middle: K

last: Kaufman

first: Song

last: Yang

middle: I


title: Assessing age-dependent effects of vhp-1 knock-down on gene expression

city: Berkeley

first: Michael

last: Shapira

address: 3060 Valley Life Sciences Bldg room 5163

department: Integrative Biology

institute: UC Berkeley

summary: Different strains of C.elegans exposed to control or vhp-1 RNAi during development or adulthood

overall_design:
12 conditions:  C. elegans, N2, kgb-1(km21), or daf-16(mu86);pmk-1(km25) exposed to control or vhp-1 RNAi during development (egg) or adulthood (L4)
2-color arrrays, each sample co-hybridized with the same reference RNA sample from mixed stage C.elegans cultures
Each condition includes 3 biological replicates with the exception of all daf-16(mu86);pmk-1(km25) conditions (2 biologial replicates) and kgb-1(km21) control RNAi_L4 which includes 4 biological replicates

first: Kwame

last: Twumasi-Boateng


title: Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data [tonsil]

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

summary: To discover new essential regulatory pathways in B lymphoma cells a combined analysis of experimental and clinical high throughput data was performed. Among others, a specific cluster of coherently expressed genes named BCR.1 was identified in primary lymphoma samples. These coherently expressed genes are suppressed by α-IgM treatement of lymphoma cells in vitro. This B cell receptor activation leads to a G2 phase prolongation, delayed entry into the M phase, an overall diminished capacity of the cells to enter into mitosis and defects in metaphases. Cytogenetic changes are detected under long term α-IgM treatment. Furthermore, an inverse correlation of BCR.1 genes with c-Myc coregulated genes in distinct groups of lymphoma patients is observed. In addition to the impact of c-Myc in the regulation of cell cycle regulators, BCR.1 genes are regulated by a combined action of IKK2, MAPK14 and JNK. Finally, the BCR.1 index discriminates activated B cell like and germinal centre B cell like diffuse large B cell lymphoma. Therefore, a new regulatory circuit is described affecting cell cycle and chromosome instability in B cells.

overall_design: 20 CD10+ B cell samples were hybridized to HGU133+2 Affymetrix GeneChips.

first: Alexandra

last: Schrader

first: Katharina

last: Meyer

first: Neele

last: Walther

first: Ailine

last: Stolz

first: Maren

last: Schmidt

first: Elisabeth

last: Hand

first: Frederike

last: von Bonin

first: Maurits

last: Evers

first: Katayoon

last: Shirneshan

first: Martina

last: Vockerodt

first: Wolfram

last: Klapper

first: Monika

last: Szczepanowski

first: Paul

last: Murray

first: Holger

last: Bastians

first: Lorenz

last: Trümper

first: Rainer

last: Spang

first: Dieter

last: Kube


title: A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma [methylation]

first: binay

last: panda

type: Methylation profiling by genome tiling array

overall_design: Bisulphite converted DNA from the 52 tumor:matched control sample pairs were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Neeraja

last: Krishnan

first: Kunal

last: Dhas

first: Jayalakshmi

last: Nair

first: Gangotri

last: Siddappa

first: Amritha

last: Suresh

first: Vikram

last: Kekatpure

first: Moni

last: Kuriakose

first: Binay

last: Panda


title: G0S2 functions as a tumor supressor through represssion of Myc signaling pathways

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 South Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois

summary: Comparions on gene expression in murine embyonic fibroblasts (MEFs) wild-type vs G0S2 null MEFs

overall_design:
Total RNA obtained from spontanously immortalized MEF cell line E2 from wild-type C57BL/6 mice (E2) and spontaneously immortalized
MEF cell line E6 from G0S2 knockout C57BL/6 mice; MEF lines were used at passage number 10-12

first: Christina

middle: Y

last: Yim


title: Transcriptomic profiling of Melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations

city: Murcia

first: Cristina

middle: Gómez

last: Aix

address: Campus universitario de Espinardo

institute: CEBAS

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

overall_design: Refer to individual Series


title: Transcriptional screening in MDA-231 cells treated with low-dose Paclitaxel for 24 and 48 hours

first: Sun

last: Lidong

state: Beijing

address: Dong zhi men nei nan xiao jie 16

institute: China Academy of Traditional Chinese Medicine

summary: Paclitaxel is the most commonly used chemotherapeutic agent in breast cancer treatment. Notably, a comprehensive understanding of paclitaxel’s effects requires insight into the dose-specific activities of paclitaxel and their influence on the cancer cells and host microenvironment. The aim of our study is to reveal the gene transcriptional changes in response to low-Paclitaxel (PTX) treatment in breast cancer cells.

overall_design: For genome-wide gene expression analysis, MDA-MB-231 cells (high-invasive breast cancer cell line) were treated with 5 ng/ml PTX for 24 and 48 hours respectively and then the cell lysates were prepared by TRIzol reagent. Then the total RNA in each group was extracted and the genome-wide gene expressing profile was detected through the Human One Array (HOA) Microarray system (Phalanx Biotech Group, Taiwan).

first: Li

last: Qi

first: Wang

last: Lu


title: Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance

city: Madrid

first: Silvana

last: Mouron

address: Calle Melchor Fdez Almagro

department: Clinical Research

institute: CNIO

summary: We sought to identify genetic variants associated with disease relapse and failure to hormonal treatment in hormone-receptor positive breast cancer (HRPBC). We analyzed a series of HRPBC with distant relapse, by sequencing pairs (n=11) of tumors (primary and metastases) at >800X. Comparative genomic hybridization was performed as well. Top hits, based on the frequency of alteration and severity of the changes, were tested in the TCGA series. Genes determining the most parsimonious prognostic signature were studied for their functional role in vitro, by performing cell growth assays in hormonal-deprivation conditions, a setting that mimics treatment with aromatase inhibitors. Severe alterations were recurrently found in 18 genes in the pairs. However, only MYC, DNAH5, CSFR1, EPHA7, ARID1B, and KMT2C preserved an independent prognosis impact and/or showed a significantly different incidence of alterations between relapsed and non-relapsed cases in the TCGA series. The signature composed of MYC, KMT2C, and EPHA7 best discriminated the clinical course, (overall survival 90,7 vs. 144,5 months; p=0.0001). Having an alteration in any of the genes of the signature implied a hazard ratio of death of 3.25 (p<0.0001), and early relapse during the adjuvant hormonal treatment. The presence of the D348N mutation in KMT2C and/or the T666I mutation in the kinase domain of EPHA7 conferred hormonal resistance in vitro.  Novel inactivating mutations in KMT2C and EPHA7, which confer hormonal resistance, are linked to adverse clinical course in HRPBC.

overall_design: Pairs of tumors (primary and metastases)

first: Luis

last: Manso

last: Tress

first: Gonzalo

last: Gómez-López

first: Manuel

last: Morente

first: Eva

last: Ciruelos

first: Miriam

last: Rubio-Camarillo

first: José

last: Rodriguez-Peralto

first: Miguel

last: Pujana

first: David

middle: G

last: Pisano

last: Quintela-Fandino


title: Shewanella piezotolerans WP3 wild-type strain heat shock for 60 min

first: Huahua

last: Jian

summary: The WP3 strains was cultured at 20°C and heat shocked at 40°C for 60 min. The transcriptional profiles after and before heat shock were compared.

first: Shengkang

last: Li

first: Fengping

last: Wang


title: Expression data of sciatic nerves from mice with Schwann-cell specific Sip1 deletion compared to control mice.

status: Public on Jun 13 2016

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary:
Schwann cell maturation is tightly controlled by a set of transcriptional regulators. We have deleted the zinc-finger transcription factor Sip1 specifically from immature Schwann cells and observed a dramatic developmental delay.
In an attempt to define the developmental stage of Sip1-deficient Schwann cells, we performed microarray analysis of Schwann cell-specific mutants compared to controls at the age of 25 days (P25).

overall_design: Sciatic nerves of 3 mutant mice and 3 corresponding controls were isolated at the age of 25 days.

first: Susanne

last: Quintes

first: Bastian

last: Brinkmann

first: Michael

last: Sereda

first: Klaus-Armin

last: Nave


title: Molecular subtypes in pancreatic adenocarcinoma [tumors, normal and pancreatitis]

city: Santa Monica

first: Habib

last: Hamidi

address: 2825 Santa Monica Blvd., Suite 200

institute: UCLA

summary: The goal of the study was to examine the transcriptional profile of pancreatic tumors to identify molecular subtypes in order to develop validated clinically useful gene expression signature with the potential to guide therapy decision.  Tissue was obtained by snap freezing in liquid nitrogen as soon as removed.   All tissue samples were stored at -80C.  Samples were embedded in OCT and a 4ug section was taken for H/E staining.   After QC procedure to ensure high quality RNA (RIN>7) and confirm PDAC histology, 78 samples were subjected to microarray analysis.   All patients signed an Institutional Review Board approved consent for bio-banking, clinical data extraction and molecular analysis.

overall_design: 85 samples (77 tumors, 3 normal and 5 pancreatitis) were compared to a mixed reference pool of 66 tumor samples to identify gene expression patterns.

first: Charles

last: Ginther

first: Lee

last: Anderson

first: Eddie

last: Garon

first: Peter

last: Schirmacher

first: Frank

last: Bergmann

first: Hsiao-Wang

last: Chen

first: Sarah

last: Dry

first: Ann

last: Mongan

first: Kim

last: Quon

first: Steve

last: Pandol

first: Dennis

last: Slamon

first: Richard

middle: S

last: Finn


title: MicroRNA-10a Regulation of Proinflammatory Mediators: An Important Component of Untreated Juvenile Dermatomyositis

city: Chicago

first: Dong

last: Xu

address: 2430 N. Halsted St.

institute: Ann & Robert H. Lurie Children's Hospital of Chicago Research Center

summary: The goals of this study are to identify differentially expressed microRNAs in muscle between JDM and normal healthy controls, and to better understand the pathophysiology of JDM.

overall_design: Global microRNA expression from the skeletal muscle of 18 children with JDM and 6 healthy pediatric controls was performed on the miRCURY LNA™ microRNA Array (6'th GEN) using Exiqon microRNA array service (Skelstedet 16, 2950, Vedbak, Denmark) and was compared to determine differentially expressed microRNAs between JDM and healthy controls.

first: D

first: L

last: Pachman


title: Ribosome quality control is a central protection mechanism for yeast exposed to Deoxynivalenol and Trichothecin

status: Public on Jun 03 2016

city: Tulln

first: Christoph

last: Schüller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology, UFT-Campus Tulln

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

summary: Trichothecenes, like deoxynivalenol (DON) are secondary metabolites of Fusarium species, and are major pollutants in cereal food and feed products. They inhibit eukaryotic protein synthesis, however with only partly resolved consequences for the cellular homeostasis. Here we report a systematic functional investigation of the effects of DON on exponential phase growing yeast cells using either short doses of DON or continuos treatment with DON.

overall_design: Yeast cells were grown in exponential phase with 0, 12 or 24ppm DON treatment and with or without a 24h 24ppm DON pre-treatment and harvested at an OD600 of 1.0 or 1.5. Experiments were performed with 3 biological replicates except for sample T0.OD1.5 which only has 2 replicates for a total of 23 samples. The 0ppm DON treatment samples were used as controls.

first: Karl

last: Kugler

first: Zeljka

last: Jandric

first: Walter

last: Glaser

first: Martin

last: Radolf

first: Marc

last: Lemmens

first: Klaus

last: Mayer

first: Gerhard

last: Adam


title: A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma

first: binay

last: panda


title: Gene expression of canine mammary cancer stem-like cells co-cultured with tumor associated macrophages

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: The aim of our study was to evaluate gene expression of canine mammary cancer stem-like cells co-cultured with tumor associated macrophages. Two canine mammary cancer cell lines (CMT-U27 and P114) were stained using  anti-Sca1 (stem cell antigen 1), anti-EpCAM (Epithelial cell adhesion molecule)  and anti-CD44 antibody. The FACS analysis showed 0,02-0,05% of Sca1+/EpCAM+/CD44+ in each of the cell line. Cancer stem-like cells were collected using FACS Aria II then  co-cultured with tumor associated macrophages and used for further analysis of gene expression ( using Agilent Gene Expression Hybridization Kit ).

overall_design: Canine mammary cancer cell lines were stained using anti-Sca1 (stem cell antigen 1), anti-EpCAM (Epithelial cell adhesion molecule) and anti-CD44 antibodies. Next using FACS Aria II and Sca1+/EpCAM+/CD44+ cells were collected and co-cultured with tumor associated macrophages. Then, total RNA was isolated and hybridized at Gene Expression microarray.

first: M

last: Krol

first: A

last: Rybicka

first: J

last: Mucha

first: B

last: Taciak


title: DNA damage regulation and its role in drug-related phenotypes in the malaria parasites. [genomic DNA]

city: singapore

first: Devendra

middle: Kumar

last: Gupta

state: Singapore

address: 60 NANYANG DRIVE

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

type: Genome binding/occupancy profiling by array

summary: The goal of our study is to characterize the global transcriptional resposne of P.falciparum to DNA damageing agents. Alongside, we stidied the epigenetic regulation  of DNA damage resposne in parasite. Further, we studied the mecanism which underlined the ARMD (mutator) phenotype of P. falciparum.

overall_design:
In order to elucidate the transcriptiona resposne to DNA damage,  P. falciparum 3D7 parasites were treated with 4 perturbating agents for 6 hours. We mapped the global nucleosome occupancy for 3 most responsive histone modifications to DNA damage by chromatin immunoprecipitation coupled with DNA microarray (ChIP-on-chip).
In order to identify the transcriptional similarities between artemesinin and MMS, we carried out 6 hours of artemesinin treatment in triplicates and compared with triplicate dataset of MMS.

first: Zbynek

last: Bozdech


title: Orf306, an esterase coded by the Organophosphate degradation (opd) island of Sphingobium fuliginis ATCC27551 induced gene expression profiling in E. coli MG1655

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

summary: Orf306 induces PNP utilization in E. coli MG1655, the gene expression studies were performed to obtain further details about proteins and pathways that are regulated under the influence of Orf306

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Organism:  Escherichia coli ,  Agilent Custom Gene Expression Escherichia Coli MG1655 8x15K ( AMADID: 019439) designed by Genotypic Technology Private Limited

first: Deviprasanna

last: Chakka

first: Dayananda

last: Siddavattam


title: Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach [miRNA microarray analysis]

city: Wuxi

first: sun

last: shengming

state: Jiangsu

address: No.9, Shanshui Rd East

country: China

institute: Freshwater Fisheries Research Center (FFRC) of Chinese Academy of Fishery Sciences (CAFS),

summary: MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs.

overall_design: In this study, Solexa deep sequencing technology was used for high-throughput analysis of miRNAs in a small RNA library isolated from four M. nipponense tissues (gill, hepatopancreas, muscle and hemocytes). In total, 9,227,356 reads were obtained, 4,293,155 of which were related to 267 unique miRNAs, including 203 conserved and 64 prawn-specific miRNAs. Furthermore, miRNA features including length distribution and end variations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways regulated by M. nipponense miRNAs. In addition, 880 co-expressed and 39 specific (25 normoxia-specific and 14 hypoxia-specific) miRNAs of four combined tissues of prawns that may be involved in the response to hypoxia were confirmed using miRNA microarray analysis. Real-time quantitative PCR (qPCR) analysis of eight miRNAs in the normoxia and hypoxia groups showed good concordance between the sequencing and qPCR data. This study provides the first large-scale identification and characterization of M. nipponense miRNAs and their potential targets, and represents a foundation for further characterization of their roles in the regulation of the diversity of hypoxia processes.

first: Shengming

last: Sun


title: Ecogenomic assessment of soil toxicity associated with the production chain of 2,5-furandicarboxylic acid (FDCA), a candidate bio-based green chemical building block

city: Amsterdam

first: Guangquan

last: Chen

address: boelelaan 1085

department: Animal ecology

country: Netherlands

institute: Vrije Universiteit

summary: 2,5-furan dicarboxylic acid (FDCA) is the top-12 value-added chemicals derived from biomass that may serve as a 'green' substitute for terephthalate acid (TPA) in polyesters. FDCA can be synthesized chemically from 5-(hydroxymethyl) furfural (HMF), which is produced from fructose or glucose. To investigate impact of the production chain of FDCA on terrestrial ecosystem and unravel molecular pathways invoked and the biological process affected in the animal, a microarray analysis was applied to measure the transcriptome-wide response in soil invertebrates Folsomia candida. Microarrays examined transcriptional changes at EC50 concentrations of FDCA, HMF and TPA spiked in sterilized LUFA 2.2 soils. The results indicated FDCA and TPA caused no significant change in gene expression, which may due to the low chemical water solubility leading to slow uptake by the animal from the pore water after. A substantial number of genes were significantly regulated in F. candida after exposure to HMF. Gene Ontology analysis showed many biological process were significantly affected, such as nucleic acid metabolism, transcriptional metabolic process, cell developmental process and oxidation-reduction process. Transcriptional profile also indicated HMF can be biotransformed by F. candida into SMF which is genotoxic and mutagenic. The current research shows that environmental risk of the FDCA production chain from biomass is not due to the final product but to the intermediate HMF.

overall_design: We used a one-color microarray design where each sample was hybridized to a single array

first: Nico

last: van Straalen

first: Dick

last: Roelofs


title: DNA damage regulation and its role in drug-related phenotypes in the malaria parasites.


title: Clonal relationship of relapsing diffuse large B-cell lymphoma

city: Basel

first: Darius

last: Juskevicius

address: Schoenbeinstr. 40

department: Molecuar Pathology

institute: Institute of Pathology

summary: Recurrences of diffuse large B-cell lymphomas (DLBCL) result in significant morbidity and mortality, but their underlying genetic and biological mechanisms are unclear. Clonal relationship in DLBCL relapses so far is mostly addressed by the investigation of immunoglobulin (IG) rearrangements, therefore lacking deeper insights into genome-wide lymphoma evolution. We studied mutations and copy number aberrations in 20 paired relapsing and 20 non-relapsing DLBCL cases aiming to test the clonal relationship between primaries and relapses, to track tumors’ genetic evolution and to investigate the genetic background of DLBCL recurrence. Three clonally-unrelated DLBCL relapses were identified (15%). Also, two distinct patterns of genetic evolution in clonally-related relapses were detected: (1) early-divergent/branching evolution from a common progenitor in 6 patients (30%), and (2) late-divergent/linear progression of relapses in 11 patients (65%). Analysis of recurrent genetic events identified potential early drivers of lymphomagenesis (KMT2D, MYD88, CD79B and PIM1). The most frequent relapse-specific events were additional mutations in KMT2D and alterations of MEF2B. SOCS1 mutations were exclusive to non-relapsing DLBCL, whereas primaries of relapsing DLBCL more commonly displayed gains of 10p15.3-p12.1 containing the potential oncogenes PRKCQ, GATA3, MLLT10 and ABI1. Altogether, our study expands knowledge on clonal relationship, genetic evolution and mutational basis of DLBCL relapses.

overall_design: There are 62 copy number Agilent  180k SurePrint arrays in total, which represent 40 cases. There are 21 arrays of primary relapsing DLBCL tumors, 21 arrys of matched relapses and 20 arrays of non relapsing DLBCLs.

first: Joel

last: Gsponer

first: Thomas

last: Lorber

first: Christian

last: Ruiz

first: Frank

last: Stenner-Liewen

first: Stephan

last: Dirnhofer

first: Aleaxndar

last: Tzankov


title: Transcriptome profiling times series of zebrafish heart regeneration

city: Luxembourg

first: Francisco

last: Azuaje

address: 84, Val Fleuri

department: Oncology

country: Luxembourg

institute: Luxembourg Institute of Health

summary: The zebrafish has the capacity to regenerate its heart after severe injury. While the function of a few genes during this process has been studied, we are far from fully understanding how genes interact to coordinate heart regeneration. To enable systematic insights into this phenomenon, we generated and integrated a dynamic co-expression network of heart regeneration in the zebrafish and linked systems-level properties to the underlying molecular events. Across multiple post-injury time points, the network displays topological attributes of biological relevance. We show that regeneration steps are mediated by modules of transcriptionally coordinated genes, and by genes acting as network hubs. We also established direct associations between hubs and validated drivers of heart regeneration with murine and human orthologs. The resulting models and interactive analysis tools are available at http://infused.vital-it.ch. Using a worked example, we demonstrate the usefulness of this unique open resource for hypothesis generation and in silico screening for genes involved in heart regeneration.

overall_design: In order to monitor the whole regeneration process, we recovered samples at different time points post-injury: 4 h, 1 day, 3 days, 7 days, 14 days and 90 days (respectively 4 hpi, 1 dpi, 3 dpi, 7 dpi, 14 dpi and 90 dpi). Cryoinjured hearts were compared to healthy hearts from control fish in 3 independent experiments.


title: DNA damage regulation and its role in drug-related phenotypes in the malaria parasites. [RNA]

first: Devendra

last: Gupta

first: Zbynek

last: Bozdech


title: DPYS as a potential diagnostic biomarker in hereditary and sporadic PRCC2

city: Singapore

first: Weng Khong

last: Lim

address: 11 Hospital Drive

department: Department of Medical Sciences

institute: National Cancer Centre Singapore

summary:
Papillary renal cell carcinoma type 2 (PRCC2) is known to be very aggressive type of tumor without effictive therapy. Hereditary form of PRCC2 is caused by Fumarate Hydratase (FH) gene mutation that accompanied Hereditary Leiomyomatosis and Renal Cell Carcinoma (HLRCC) disorder. In sporadic form of PRCC2 the mutation of FH gene has not been reported. Both forms of tumors have the similar histopathological characteristics with poor survival prognosis.
In this study, we profiled the gene expression of renal tumors and normal tissue from PRCC2 (hereditary and sporadic) patients in order to better understand commonalities and differences in the transcriptional landscape of PRCC2.

overall_design: Microarray gene expression profiling was performed on eight normal kidney tissue samples, five hereditary PRCC2 tumor tissue samples and 19 sporadic PRCC2 tumor tissue samples. Hereditary PRCC2 (HPRCC2) patients were confirmed by DNA sequencing of the FH gene.

first: Victoria

last: PERRIER-TRUDOVA

first: Aikseng

last: OOI

first: Weng

last: LIM

first: David

last: PETILLO


title: Growth arrest of human thyroid cancer cells 8505C after inhibition of TTF-1 transcriptional activity

city: Gosselies

first: Christiane

last: Christophe-Hobertus

address: Biopark Charleroi Brussels South,

department: IBMM

institute: Université Libre de Bruxelles

summary: Background: thyroid transcription factor-1 (TTF-1) is known to play key roles in thyroid organogenesis, in thyroid cell proliferation and in the expression of genes involved in thyroid differentiated function.   Objective: to understand why many human thyroid cancer cell lines keep producing TTF-1 despite the loss of differentiation.   Methods: a chimeric protein acting as a functional antagonist of TTF-1 transcriptional activity was expressed conditionally in 8505C cells originating from an undifferentiated thyroid carcinoma. The consequences of the inhibition of TTF-1 activity in the cells expressing the antagonist on cell proliferation, mRNA and miRNA expression were analyzed.  Results: we observed a growth arrest of 8505C thyroid cancer cells when the endogenous TTF-1 transcriptional activity was inhibited. It correlated with decreased levels of several mRNAs encoding positive effectors of cell proliferation like CDK1 and cyclinB1, and increased levels of various mRNAs encoding negative regulators of cell division like CDKN2B and DUSP6. By contrast, no significant change was observed in the miRNA population.  Conclusion: the persistence of TTF-1 expression observed in most dedifferentiated human thyroid cancer cell lines is likely to be explained by the fact that TTF-1 activity is still required for proliferation of these tumor cells as demonstrated here in the 8505C cell line.

overall_design: Microarrays miRNA hybridizations were performed on 8505c cells expressing a TTF1 antagonist (Engr HD –Dox) versus non-expressing cells (Engr HD +Dox), on cells expressing the control protein (Engr HDm – Dox) versus non-expressing cells (Engr HDm + Dox), and on cell expressing the TTF1 antagonist (Engr HD– Dox) versus the cells expressing the control protein (Engr HDm– Dox). Hybridizations were replicated with dye swap.

first: Manuel

last: Saiselet

first: Anne

last: Lefort

first: Jacques

last: Dumont

first: Carine

last: Maenhaut

first: Frederick

last: Libert

first: Daniel

last: Christophe


title: IL-18 nAbs block deleterious inflammatory cytokines induced by acute β-AR stimulation in heart

status: Public on May 31 2016

city: Beijing

first: Hao

last: LI

address: No. 49, Huayuan Bei Road, Haidian District

department: Institute of Vascular Medicine

institute: Peking University Third Hospital

summary: To directly test whether inhibition of IL-18 by IL-18 neutralizing monoclonal antibodies (IL-18 nAbs)  is sufficient for blocking the inflammatory responses of heart caused by acute β-adrenergic insult, mice were subjected to intraperitoneal injection with rat IL-18 nAbs or IgG as a negative control 1hr after isoproterenol treatment.

overall_design: 16 samples. There are 4 groups: vehicle group, mice were subcutaneous injected with a single dose of saline (10 ml/kg body weight), ISO group, mice were subcutaneous injected with a single dose of isoproterenol (5 mg/kg body weight). ISO+IL-18 nAbs group, IL-18 nAbs were intraperitoneally injected (50 μg/ mouse) at 1 hr after ISO injection. ISO+IgG group, rat IgG were intraperitoneally injected (50 μg/ mouse) at 1 hr after ISO injection. The hearts from mice were harvested at 24 hrs after saline or ISO treatment.

first: Youyi

last: ZHANG


title: Oxidative quality control regulates response to ER stress through translation control

first: Genotypic

last: technology

summary: The transcriptomic response after 3 hours of DTT treatment shows there is not a drastic difference in most genes between WT and skn7∆, yap1∆ . Vma13∆, sse2∆ were also used as part of the study.

overall_design: Organism : Saccharomyces cerevisiae,  Agilent Yeast Gene expression 8x15K Array AMADID: 016322

first: Shuvadeep

last: Maity

first: Kausik

last: Chakraborty

first: Asmita

last: Ghosh

first: Shantanu

last: Sengupta


title: Effect of maternal treatment on gene expression differences in Bacillus thuringiensis infected pooled larvae

city: Princeton

first: Ann

middle: Thomas

last: Tate

state: NJ

address: 106A Guyot Hall

department: Ecology and Evolutionary Biology

institute: Princeton University

summary:
This study examines gene expression differences between infected larvae from different maternal infection backgrounds to try to understand the immunological basis of invertebrate immune priming. Female Tribolium castaneum beetles were either jabbed with sterile saline, heat killed Bt, or left naïve. 15 Offspring from the first and second broods were infected with Bt and 24 hours later pooled by treatment and flash frozen
Beetles from saline and primed maternal backgrounds are compared to naïve infected

overall_design: Pooled whole larvae, custom array for T. castaneum, 1 replicate per treatment comparison. Same naïve sample used for both arrays

middle: T

first: Peter

last: Andolfatto

first: Andrea

middle: L

last: Graham


title: Gene expression levels dependent on cultivated temperature

city: Kobe

first: Atsushi

last: Kuhara

state: Hyogo

address: Okamoto8-9-1, Higashinada-ku

department: Biology,  Faculty of Science and Engineering

country: Japan

institute: Konan University

summary: To evaluate the gene expression levels dependent on cultivated temperature (15-degree only or 25-degree after 15-degree grown) in wild type (N2 strain) and daf-2mutant

overall_design: Worms were cultivated at 15-degree from egg to adult or at 25-degree for 12 hours after 15-degree grown until young adult, then total RNA was collected

first: Satoru

last: Sonoda


title: Transcriptional Response of Mycobacterium tuberculosis to Growth without Detergent

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv grown in minimal media with or without detergent for 5 days to investigate basis of differences in vaccine efficacy dependent on growth conditions

overall_design: Two condition experiment, detergent grown vs. grown without detergent. Biological replicates: 3 of each condition, independently grown and harvested. One replicate per array, third array is a dye-flip.

first: Rafael

last: Prados-Rosales


title: Interconnections between RNA-processing pathways revealed by a sequencing-based genetic screen for pre-mRNA splicing mutants in fission yeast

status: Public on May 02 2016

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

summary: Splicing profiling of deletion strains compared to wild-type control

overall_design: Splicing sensitive S. pombe microarrays (Agilent-027365) were used to compare the splicing profile of various deletion strains relative to wild-type.

first: Amy

last: Larson

first: Benjamin

last: Fair