title: Expression data from internodes of maize seedlings

city: Beijing

first: weiqiang

last: zhang

address: No 2 Yuanmingyuan Xi Lu, Haidian District

institute: China Agricultural University

summary:
Plant growth regulators (PGRs) were commonly used in practical farming to restrict plant height and control lodging. Ethephon has been reported to shorten the internodes elongation and increase the harvestable grain yield of maize. In the present study, we characterized that internodes phenotypic responses to ethephon treatment induced should due to ethylene released inhibited the longitudinal growth of cells and promoted its the lateral growth.
We used microarrays to detail the global programme of gene differentially expression underlying maize and identified distinct classes of up or down-regulated genes during this process.

overall_design: After ethephon sprayed treatment 0 day (0 h), 1 day (24 h), 2 day (48 h), the seventh internode of maize seedlings from the treatment group and control were collected. The internodes meristem were frozen immediately using liquid nitrogen and stored at -80℃ for further RNA extraction. Every RNA sample was derived from 3 independent seedlings. In sum, three time points were selected and three biological replicates were performed at each time point, totally 15 maize genome arrays were used.

first: Xiaoyi

last: Wei

first: Weiqiang

last: Zhang

first: Liusheng

last: Duan


title: Identification of regulatory targets of the cereal VERNALIZATION1 transcription factor

status: Public on Jan 01 2017

city: Canberra

first: Ben

last: Trevaskis

state: ACT

address: Clunies Ross Drive

department: Plant Industry

country: Australia

institute: CSIRO

summary: Affymetrix Barley1 chip (GPL1340) was used to assay gene expression in RNA from barley seedlings, minus roots, at the 2-leaf stage. Expression was compared between plants carrying a VRN1-HA fusion construct (3 replicates) versus sibling null lines that lack the transgene.

overall_design: 6 samples, 3 replicates with transgene (b1-b3), 3 replicates of negative control line (a1-a3)

first: Weiwei

last: Deng


title: Analysis of gene expression profiles of the cold-inducible RNA-binding protein knockdown BHK21 (Cirp−/−BHK21) cells

city: Chengdu

first: Cheng

last: TANG

state: Sichuan

address: No 16  Yihuan Lu South Sect.4,

country: China

institute: Southwest University for Nationalities

summary: In this study,  We analyzed the gene expression of Cirp−/−BHK21 cells at different timepoint using Mus musculus genome-wide expression microarrays to explore the molecular mechanism of Cirp action.

overall_design: Total of 18 samples were detected  between Cirp−/−  and control BHK21 cells at 24h,48h and 72h three timepoint using  Mus musculus genome-wide expression microarrays, three repeats of Cirp−/− and control were detected at each timepoint.


title: The miRNA profiling in  PANC-1, PANC-1 GEM 100 and PANC-1 GEM1500 cells

status: Public on Dec 31 2016

city: Miaoli County

first: Jen-Liang

last: Su

address: No.35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan.

country: Taiwan

institute: National Health Research Institutes

summary: Gemcitabine has been a first-line therapeutic agent for pancreatic ductal adenocarcinoma (PDAC) pancreatic cancer; however, acquisition of resistance to gemcitabine remains a major challenge. We analyzed miRNAs expression profiles by array-based miRNAs analysis between gemcitabine–resistant (PANC-1/GEM) and parental PANC-1 cells.

overall_design: The three PDAC cells including PANC-1, PANC-1 GEM 100 and PANC-1 GEM1500 were harvested and RNA were isolated. Two independent experiments were performed for each group.

first: Su

last: Yen-Hao


title: Lead (Pb+2) effects in global gene expression in the larval brain of Drosophila melanogaster

city: Gurabo

first: Adrinel

last: Vázquez Montes

state: PR

address: 189 Road Km 3.3

department: Biology

country: Puerto Rico

institute: SUAGM

summary: Lead (Pb2+) is an environmental contaminant that is widely distributed around the world, mainly due to anthropogenic sources.  Developmental exposure to Pb2+ has been linked to neurodevelopmental impairments in different animal species.  Studies have shown that developmental exposure to Pb2+ could interfere with normal gene expression patterns in the immature brain leading to neurodevelopmental neuropathologies. However, the precise molecular mechanisms underlying the neurotoxicity of developmental Pb2+ exposure are still to be elucidated.  We used the fruit fly to gain insights into the molecular mechanisms affected by exposure to this neurotoxicant. The fruit fly, has been used recently to understand the behavioral, synaptic and molecular changes after developmental exposure to Pb+2. Our overarching hypothesis is that developmental exposure of the fruit fly to Pb+2 results in global gene expression dysregulation in the larval brain resulting in central nervous system developmental impairments.  We collected RNA samples from larval brain of control and Pb2+-exposed flies and performed cRNA hybridization on a 4x44K Agilent microarray.  Overall, Pb+2 results in transcriptional disturbances of important developmental signaling pathways in the larval brain.

overall_design: The experimental design consisted of four microarray experiments. Cy-5 labeled cRNA control targets were combined with Cy-3 labeled cRNA experimental (Pb+2) targets obtained from brains of wandering third instar larvae. The combined Cy-5 and Cy-3 cRNAs targets were used for probe hybridization onto the first and third microarray, respectively. Dye swapping was done using different biological replicates for both Cy-3 labeled control targets and the Cy-5 Pb+2 targets (as above) and used for hybridization on the second and fourth microarray respectively. Dye swaps using different biological replicates were done to correct for any dye-bias.

first: Humberto

last: Ortiz-Zuazaga

last: Vazquez-Montes

first: Sandra

last: Peña de Ortiz

first: Amneris

last: Hernández

first: Jorge

last: Ortiz-Carpena

first: Charlton

last: Díaz


title: Arabidopsis thaliana seedlings: Wild type vs. zrf1 mutants

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

summary: Transcriptional profiling of 6-day-old seedlings of Arabidopsis wild type control and zrf1 mutants is performed using Agilent's Whole Arabidopsis Gene Expression Microarray (4x44K).

overall_design: Two-condition experiment: seedlings of wild type control vs. mutant zrf1a-1 zrf1b-1 or zrf1a-2 zrf1b-1 seedlings. Biological replicates: 3 control, 3 zrf1a-1 zrf1b-1 mutant and 2 zrf1a-2 zrf1b-1 mutant, independently grown under 12h light/ 12h dark photoperiods and harvested.

first: Wen Hui

first: Jing

last: Feng

first: Yu

last: Yu


title: Genome-wide analysis of copy number variations in Chinese sheep using array comparative genomic hybridization

city: Hohhot

first: Li

last: Ru

address: Saihan Road 306

institute: Inner Mongolia University

type: Genome variation profiling by genome tiling array

summary:
CNVs have been recognized as a very important source of genetic variability.Some CNVs have been shown to play an important role in gene expression and impact phenotypes.
The aCGH experiment was used to obtain a sheep map of CNVs based on the ovine genome.

overall_design: comparison of Kazakh sheep, two Mongolian sheep, Tibetan sheep, Hu sheep against Dorper sheep reference

first: Yanru

last: Zhang

first: Huanming

last: Zhou


title: Pre- and Post-hatch transcriptomic response of chicken Musculus pectoralis major to transient variation of incubation temperature

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

summary: After elevated and reduced incubation temperature during embryonic days (ED) 7-10 and 10-13 changes of gene expression were determined  at ED 10, ED 13, and post-hatch at day (D) 35

overall_design: Broiler eggs were incubated at a lower or higher temperature (36.8°C, 38.8°C) relative to control (37.8°C) over two developmental intervals, embryonic days (ED) 7-10 and 10-13. Global gene expression of Musculus pectoralis major was assayed at ED 10, ED 13, and slaughter age [post-hatch day (D) 35] (6 groups; 3 time points; 8 animals each) by microarray analysis and treated samples were compared to controls within each time point

first: Watcharapong

last: Naraballobh

first: Nares

last: Trakooljul

first: Eduard

last: Muráni

first: Siriluck

last: Ponsuksili


title: Human leiomyosarcoma samples, molecular classification

city: London

first: YF

last: Lee

address: 15 Cotswold Rd

country: United Kingdom

institute: Institute of Cancer Research

summary:
Molecular classification of human leiomyosarcomas
To identify new molecular subgroups

overall_design: Two-colour microarray experiments, fresh-frozen tumour samples were used.  Tumours were Cy5 labelled, control RNAs from cell lines were Cy3 labelled.

first: Y

middle: F

first: T

last: Roe

first: I

last: Judson


title: To study global expression profile of adult zebrafish in response to arsenic trioxide

city: Delhi

first: Atish

last: Ray

state: Delhi

address: North Campus - in front of VP Chest Institute

department: Zoology

country: India

institute: University of Delhi

summary: Present experinment depicts the global gene expression profile of adult zebrafish to understand the conserved molecular snapshot beyond dose dependency and tissue specificity. The data provides ample insight of changes in gene expression leading to arsenic toxicity in vivo. Several aspects of arsenic toxicity are further validated by qPCR.

overall_design: Agilent Custom Zebra fish 8x60k Gene Expression  (AMADID: 64074) designed by Genotypic Technology Private Limited, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442). Arsenic induced gene expression was mesured in control and exposed (20ppb, 40ppb, 80ppb) zebrafish. Assay were perfomed with thecnical duplicate. Each replicate comprices of pooled RNA from three different individuals chosen randomly.


title: Host- parasite interaction: Transcriptome responses to parasitism in the silkworm Bombyx mori

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

summary: To reveal the variations in transcriptome responses of hemocytes of B. mori after the parasitic infection.

overall_design: Organism : Bombyx mori , Agilent Custom Silkworm Gene Expression  4x44k Array (AMADID: 066047) designed  by Genotypic Technology Private Limited.

first: A

middle: R

last: Pradeep

first: Pooja

last: Makwana

first: P

middle: H

last: Shambhavi


title: Zinc-Induced Transposition of Insertion Sequence Elements Contributes to Increased Adaptability of Cupriavidus metallidurans

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

type: Expression profiling by genome tiling array

summary:
Bacteria can respond to adverse environments by increasing their genomic variability and subsequently facilitating adaptive evolution. To demonstrate this, the contribution of Insertion Sequence (IS) elements to the genetic adaptation of Cupriavidus metallidurans AE126 to toxic zinc concentrations was determined. This derivative of type strain CH34, devoid of its main zinc resistance determinant, is still able to increase its zinc resistance level. Specifically, upon plating on toxic zinc medium, resistant variants arose in which a compromised cnrYX regulatory locus caused derepression of CnrH sigma factor activity and concomitant induction of the corresponding RND-driven cnrCBA efflux system. Late-occurring zinc resistant variants likely arose in response to the selective conditions, as they were enriched in cnrYX disruptions caused by specific IS elements whose transposase expression was found to be zinc-responsive.
Interestingly, deletion of cnrH, and consequently CnrH-dependent adaptation potential, still enabled adaptation by transposition of IS elements (ISRme5 and IS1086) that provided outward-directed promoters driving cnrCBAT transcription. Finally, adaptation to zinc by IS reshuffling can also enhance the adaptation to subsequent environmental challenges. Thus, transposition of IS elements can be induced by stress conditions and play a multifaceted, pivotal role in the adaptation to these and subsequent stress conditions.

overall_design: Comparison of wild-type or knock-out strains with evolved strains resulting from a lab evolution experiment

first: Joachim

last: Vandecraen

first: Pieter

last: Monsieurs

first: Max

last: Mergeay

first: Natalie

last: Leys

first: Abram

last: Aertsen


title: Transcriptional Profiling of Zebrafish Embryonic Developmental Time Course

city: Brisbane

first: Charles

middle: Cameron

last: Bell

state: Queensland

address: 37 Kent Street

institute: Mater Research

summary: Coordinated cell movements of gastrulation reshape the uniform blastula into a structured gastrula with three fundamental axes and an internal germ layer of mesoderm. Genetic regulation of the forces which drive gastrulation is incompletely understood. We employed a microarray screen in zebrafish for genes which are dynamically expressed during embryonic development. In particular, we were interested in exploring genes that are expressed during the gastrulation.

overall_design: No biological replicates were performed. Each of the nine time points was co-hybridized with a reference sample made by pooling RNA from each time point. The microarray schema incorporated dye swapped hybridizations to account for dye bias.

first: Simon

middle: J

last: Wilkins

middle: C

first: Karin

last: Kassahn

first: Brooke

middle: B

last: Gardiner

first: Darrin

last: Taylor

first: Cas

last: Simons

first: Sean

middle: M

last: Grimmond

first: Andrew

last: Perkins


title: Mtx2 dependent genes during Zebrafish gastrulation

summary: Transcriptional profiling of Mtx2 morphants at 30% epiboly stage, shield stage and tailbud stage of embryonic development: Coordinated cell movements of gastrulation reshape the uniform blastula into a structured gastrula with three fundamental axes and an internal germ layer of mesoderm. Genetic regulation of the forces which drive gastrulation is incompletely understood. We employed a microarray screen in zebrafish for genes which participate in epibloy, and identified many with biochemical roles in endocytosis, microtubule remodeling, cell adhesion and transcription.

overall_design: For direct comparisons between mtx2 MO and std MO treated embryos, pair-wise hybridizations were performed for each of the three time points. For the shield and tailbud stage five biological replicates were generated for hybridization. Twelve biological replicates were generated for hybridization for the 30% epiboly stage. The microarray schema incorporated dye swapped hybridizations to account for dye bias.


title: Integration of miRNA, mRNA and methylation profiling reveals genes aberrantly regulated associated to RETM918T mutation in Medullary Thyroid Carcinoma

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Integration of miRNA, mRNA and methylation profiling reveals genes aberrantly regulated associated to RETM918T mutation in Medullary Thyroid Carcinoma [miRNA component]

summary: Medullary thyroid carcinoma (MTC) accounts for 1-2% of thyroid malignancies. It is a disease of few genetic drivers, and the etiology specifically associated with each mutation remains unknown. Here, we investigated the role of aberrant DNA methylation in the MTC development. We performed genome-wide DNA methylation profiling assessing >27,000 CpGs in the largest MTC series reported to date, comprising 48 molecularly characterized tumors. We observed significant differences between the methylation patterns among the samples bearing the RETM918T, RETC634 mutation and “wild-type” (WT) tumors, but not those RAS-related. In detail, the RETM918T –related tumors had a larger number of hypomethylation events when compared to RETC634 – positive and WT ones. Moreover, through the integration of methylation with mRNA and miRNA expression data of the same tumors, we identified genes whose expression is negatively correlated with the methylation status of their promoters. For PLCB2, DKK4, MMP20 as well as miR-10a, -30a and -200c, the impact of promoter methylation levels on expression of these genes in MZ-CRC-1 and TT cell lines was assessed.  Finally, the aberrant methylation validation of three of the genes in an independent set of 25 MTCs by bisulfite pyrosequencing suggests their role as MTC methylation markers.

overall_design: For each of the MTC tumors used for profiling, 300 ng of total RNA was amplified, then labeled with Hy3 fluorescent dye and hybridized over 16 h at 56°C onto a miRNA microarray (Exiqon, v.11.0-hsa, mmu & rho) according to the manufacturer’s instructions using miRCURY LNATM microRNA Array kit (Exiqon). The slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

first: Veronika

last: Mancikova

first: Iñaki

last: Comino-Mendez


title: Integration of miRNA, mRNA and methylation profiling reveals genes aberrantly regulated associated to RETM918T mutation in Medullary Thyroid Carcinoma [methylation component]

overall_design: Bisulphite converted DNA from 48 medullary thyroid carcinoma samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2


title: Expression data from root segments of barley (Hordeum vulgare) during a transient water deficit repressing lateral root formation

city: Louvain-la-Neuve

first: Xavier

last: Draye

address: Croix du Sud 2- L7.05.11

department: Earth and Life Institute

institute: Université catholique de Louvain

summary:
In the lateral root repression system described by Babé et al. (2012), the first asymetric divisions of pericycle cells preceding lateral root formation are repressed during water deficit treatments. During an 8-hr long treatment, an 8-mm long root segment is formed where LR formation has been repressed.
The experiment was designed to monitor changes in gene expression during early events of LR formation in barley using this LR repression system.

overall_design: In barley, the first assymetric division occurs ca. 12 mm proximal from the root tip, while the next divisions occur ca. 20 mm from the tip. A sample length of 5 mm was chosen, as a compromise between maximising the amount of RNA per sample and minimising the probablity to capture cells undergoing the second round of divisions. The sampling strategy was designed to monitor gene expression at -4, -2, 0, 2 and 4 hours relative to the first asymetric division, in conditions that enable (A, control, plants watered normally) or repress (B, water deficit WD) LR formation. 5-mm long segments were sampled such that the first sampling (-4h position) targets a region distal to the first asymetric divisions, and the last sampling (+4h position) targets a region proximal to the first asymetric division.

first: Tristan

last: Lavigne

first: Boris

last: Parizot


title: Gene Expression Profile of app1Δpah1Δdpp1Δlpp1Δ

first: Malathi

last: Srinivasan

address: Allalasandra, GKVK Post, Bellary Road

department: Lipidomic Center

institute: Central Food Technological Research Institute

summary: Deletion mutant of the yeast app1Δpah1Δdpp1Δlpp1Δ were studied for gene expression levels. Significant difference in expression levels was observed in genes pertaining to mitochondria, lipid etc. as compared to the W303-1A wild type.

overall_design: Organism : Saccharomyces cerevisiae , Custom Saccharomyces cerevisiae 8x15k Gene expresssion Microarray (AMADID: 016333) designed by Genotypic Technology Private Limited

first: D

last: Kanagavijayan

first: M

first: R

last: Rajasekharan


title: Virulence associated genes in Streptococcus uberis

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

institute: RMIT University

summary: Infection caused by bacteria from environmental reservoirs such as E. coli and S. uberis have not decreased in prevalence. Lack of success in controlling bovine mastitis due to S. uberis is associated with the route of infection which is not well understood and there is inadequate information on pathogenesis of S. uberis. Therefore, this study was to investigate the virulence factors of S. uberis using comparative genome analyses using isolates from cows with clinical mastitis and isolates from cows with a low cell count in their milk using a Subtracted Diversity Array (SDA). This study also reports the construction and validation of a microarray capable of fingerprinting the virulent and non-virulent isolates using the SDA technique.

overall_design: DNA of 29 non-virulent strains and virulent strains was subtracted from pooled genomic DNA of 12 S. uberis strains. 280 subtracted DNA fragments were used to construct S. uberis-specific array. The validation of S. uberis-specific array revealed a high (77%) subtraction efficiency. 29 S. uberis strains, representing 20 clinical isolates and 9 low cell counts were hybridized onto the array to reveal its level of strain discrimination based on the prevalence and virulence specificity for each S. uberis tested strain. All these species could be successfully differentiated using their hybridization patterns. 26 probes were characterized by sequencing. A number of probes were novel virulence associated gene whilst some of them could indicate their essential roles as virulence factors.

first: Salem

last: Abureema

first: Margaret

last: Deighton


title: Gene expression levels in Arid1a deficiency mice liver and their littermates

city: Shanghai

first: Ze Guang

last: Han

address: No. 197 Second Rui Jin Rd.

institute: Key Laboratory of Systems Biomedicine (Ministry of Education) of Rui-Jin Hospital

summary: ARID1A encodes a subunit of chromatin remodeling SWI/SNF complexes and has recently been suggested to be a tumor suppressor gene based on its loss of function somatic mutations, which are frequently found in various human tumors, including hepatocellular carcinoma (HCC). However, the role and mechanism underlying ARID1A mutations in tumorigenesis remain unclear. Here we show that hepatocyte-specific Arid1a deficiency in mice results in steatohepatitis and HCC development, which are accompanied by increased DNA damage, hepatocyte death, mitochondrial damage, innate immune cell infiltration, and large-cell dysplasia, as well as proinflammatory cytokines, TNF-alpha and IL-6 production, and activation of the STAT3 and NF-kappaB pathways. Interestingly, we found that Arid1a ablation-mediated hepatocyte death and liver inflammation are dependent upon Tp53-Bax proapoptotic signaling. In the absence of Tp53, hepatocyte death, immune cell infiltration, and TNF-alpha and IL-6 production were significantly decreased. This study provides an alternative mechanism by which Arid1a deficiency or loss of function mutations contributes to tumorigenesis.

overall_design: At each time point (5 day, 2 week and 1 month) total liver RNA from 2 individual mice (2-week-old mice only contain one in each group) was compared to pooled total liver RNA from time-matched control mice (n = 2).

first: Ze-Guang

first: Jia-Zhu

last: Fang


title: The expression level of microRNA after knockdown of ATMIN in SW620 cells

city: Taipei City

first: Yueji

last: Li

address: No.7, Zhongshan S. Rd., Zhongzheng District,

institute: National Taiwan University

summary: To screen the microRNA regulated by ATMIN

overall_design: Establish stable transfectants of pLKO-sh-ATMIN in SW620 cells and analyze the miRNA expression level of  by microRNA microarray. SW620 transfected with pLKO-sh-scr was used as a control experiment.

first: Cheng-Chi

last: Chang

first: Yue-Ju


title: Expression profile in response to sphingolipid

city: saga city

first: Hiroshi

last: Kitagaki

address: 1, Honjo-cho

country: Japan

institute: Saga University

summary: In order the obtain information which genes are differentially expressed in response to glucosylceramide

overall_design: GC of hen of the woods and soybean were added at 40 ug/ml to yeast cells, incubated for 17 h and total RNA was extracted.


title: The expression level of microRNA after knockdown of ATMIN

overall_design: Establish stable transfectants of pLKO-sh-ATMIN in HCT116 cells and analyze the miRNA expression level of  by microRNA microarray. HCT116 transfected with pLKO-sh-scr was used as a control experiment.


title: Elucidating drug mechanistics and resistance in HER2-positive breast cancer cell lines by mathematical modeling

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

institute: German Cancer Research Center

summary: Advancing precision medicine in the field of cancer is still curbed by the fact that a rational basis to predict treatment outcome is missing. To unravel the mechanism behind targeted drugs (trastuzumab, pertuzumab, erlotinib), mathematical modeling employing ordinary differential equations (ODE) was combined with wet-lab experimentation. Experimentation relied on systematic perturbation experiments to monitor the signaling-response towards drugs in the context of EGF signaling in the HER2+ cell lines SKBR3 and HCC1954.

overall_design: The impact of three different targeted drugs (trastuzumab, pertuzumab, erlotinib) on the breast cancer cell lines SKBR3 and HCC1954 was analyzed in a time-resolved manner. Each perturbation was performed as biological triplicate and the expression level of 31 different protein/phosphoproteins was monitored using reverse phase protein arrays. The selected protein/phosphoproteins are all part of the EGF signaling pathway.

first: Daniel

last: Kaschek

first: Johanna

last: Sonntag

first: Frauke

last: Henjes

first: Silvia

last: von der Heyde

first: Christian

last: Quack

first: Stefan

last: Wiemann

first: Max

last: Hasmann

first: Tim

last: Beißbarth

first: Jens

last: Timmer


title: Characterizition of a fast-growing Lactococcus lactis mutant on maltose

city: Kgs. Lyngby

first: Jun

last: Chen

state: Denmark

address: Søltofts Plads Building 221

department: Food

country: Denmark

institute: The Technical University of Denmark

summary:
Trade-offs often occurs during experimental evolution. For example, the degeneration of growth in glucose was found in a galactose adapted yeast. Here, we isolated one Lactococcus lactis mutant using experimental on maltose. The mutant grows normally on glucose, but faster than the wild-type on maltose and galactose.
DNA microarray analysis and whole genome re-sequencing were applied to disclose the crucial points that determine the phenotype.

sample_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: MG1363 versus CS3155 on glucose, maltose and galactose

first: J

first: S

last: Chan

last: Shen

first: P

last: Jensen

first: C

last: Solem


title: Gonadal gene expression in a fish with genetic and environmental sex determination under thermal and chemical pollution

city: Barcelona

first: Noelia

middle: T

last: Díaz Blanco

state: Barcelona

address: Passeig Marítim de la Barceloneta 37-49

department: Marine Renewable Resources

institute: Institute of Marine Sciences (ICM-CSIC)

summary: Understanding the consequences of thermal and chemical variations in aquatic habitats is of importance in a scenario of global change. In ecology, the sex ratio is a major population demographic parameter. Research carried out so far on environmental perturbations on fish sex ratios has usually involved a few model species with a strong genetic basis of sex determination, analyzing juvenile or adult gonads. However, the underlying mechanisms at the time of commitment are poorly understood. The European sea bass has a mixed genetic and environmental sex determination system, which makes it naturally sensitive to environmental cues. Here, we transcriptomically analyzed developing gonads experiencing either testis or ovarian differentiation as a result of thermal and/or estrogen influences. Elevated temperature masculinized genetic females while estrogen exposure resulted in an all-female population. A total of 383 genes were differentially expressed, with an overall downregulation in the expression of genes involved both in testicular and ovarian differentiation in the estrogen-exposed fish achieved by a shutdown of the first steps of steroidogenesis. GO enrichment analysis uncovered affected pathways related to the immune response, xenobiotic metabolism, response to stimulus, signaling and growth. However, once the female phenotype was imposed gonads could continue their normal development, even taking into account that some of the resulting females were fish that otherwise would have developed as males. The data on the underlying mechanisms operating at the molecular level presented here contributes to better understanding the sex ratio response of fish species subjected to a combination of environmental perturbations.

overall_design: Whole gonad transcriptome analysis from 10 individuals: 5 individuals early reared at a low temperature (15°C) and 5 individuals early reared at high temperature (21°C) all of them submitted to a feminizing treatment by Estradiol administration between 90 and 154 days post hatch.

last: Díaz

first: Francesc

last: Piferrer


title: p120-catenin differentially regulates cell migration by Rho-dependent intracellular and secreted signals

first: Mirna

middle: Alicia

last: Perez-Moreno

address: 3rd Melchor Fernandez Almagro st

department: Epithelial Cell Biology

institute: CNIO

summary: The Adherens Junction protein p120-catenin is implicated in the regulation of cadherin stability, cell migration and inflammatory responses in mammalian epithelial tissues. How these events are coordinated to promote wound repair is not understood. We show that p120-catenin regulates the intrinsic migratory properties or primary mouse keratinocytes, but also influences the migratory behavior of neighboring cells by secreted signals. These events are rooted in the ability of p120-catenin to regulate RhoA-GTPase activity, which leads to a two-tiered control of cell migration. One restrains cell motility via increase of actin stress fibers, reduction in integrin turnover, and an increase in focal adhesions robustness. The other is coupled to the secretion of inflammatory cytokines including Interleukin-24, which causally enhances randomized cell movements. Taken together, our results indicate that p120-RhoA-GTPase-mediated signaling can differentially regulate the migratory behavior of epidermal cells, which has potential implications for chronic wound responses and cancer.

overall_design: Total RNA from the backskin of p120L/L -K5Cre+/+ or p120Δ/Δ -K5Cre+/T mouse embryos (E18.5) was isolated. The RNA quality (between 6.7 to 8.8) was confirmed using an Agilent 2100 Bioanalyzer. The amount of nucleic acid labeled was 1 µg and amplification was performed using the Commercial Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit following the manufacturer’s instructions. (Agilent manual G4140-90050 Ver. 5.7 March 2008.) The microarray used was Mouse WMG 4X44K (Agilent microarray design ID 014868, P/N G4122F). The amount of each labeled nucleic acid extracted was 825 ng in a final volume of 100 µl. The hybridization was performed at 65 ºC for 17 h and the scan was performed on a G2565C DNA microarray scanner (Agilent). Images were quantified using the Agilent Feature Extraction Software (ver. 10.1.1).

first: Carolina

last: Epifano

first: Diego

last: Megias


title: miRNA expression profiles in nasal NK-cell lymphoma

city: Taipei

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

department: Pathology

summary: Nasal NK-cell lymphomas are EBV-infected lymphomas of the nasal mucosa. The genome-wide miRNA expression profiles of 36 cases of NNLs are determined with the NanoString technology. It is found that the expression levels of let-7 inhibits progression of nasal lymphomas.

overall_design: The nCounter miRNA Expression Analysis System (NanoString Technologies, Seattle, WA) was used to obtain the expression profiles of 654 human miRNAs, and a panel of 6 synthetic miRNAs as internal positive controls. Approximately 0.1 μg of total RNAs were extracted from from formalin-fixed paraffin-embedded tissue blocks. Mature miRNAs were ligated to sequence-specific miRtags, and the miRtagged mature miRNAs were hybridized to fluorescent reporter probes and to capture probes. After hybridization, the samples were immobilized to a solid-phase cartridge, and a CCD digital analyzer was used for data acquisition.


title: Gene expression profiles in group G streptococci under various stress conditions

city: Tokyo

first: Shinya

last: Watanabe

address: 1-21-1 Toyama

department: Department of Infectious Diseases

institute: National Center for Global Health and Medicine

summary: Background: Streptococcus dysgalactiae subsp. equisimilis (SDSE), similar to Lancefield group A Streptococcus pyogenes (GAS), causes invasive diseases such as life-threatening streptococcal toxic shock syndrome (STSS). Despite their similar genome sequences, SDSE lacks several important virulence factors of GAS, suggesting that SDSE has specific disease-causing systems. Using microarray analysis, we analyzed SDSE for specific transcriptional regulatory systems involved in stress responses, such as the LytSR/LrgAB system, and their transcriptional profiles under stress conditions.  Methods: Transcriptional profiling was performed using microarrays to test the effects of eight antibiotics and five growth conditions. These findings were compared with those obtained during intraperitoneal infection in mice.   Results: Genes encoding LrgAB, which modulates the murein hydrolase activity of CidAB and inhibits autolysis in Staphylococcus aureus, were upregulated by exposure to antibacterial agents, phosphate buffered saline (PBS) and stationary phase conditions and during intraperitoneal infection in mice. Starvation and anaerobic conditions stimulated the expression of the streptolysin S operon and polysaccharide lyases in SDSE. Catabolite-responsive elements (cre) were present in the promoter regions of these genes, suggesting that carbon catabolite repression (CCR) is involved in regulating SDSE virulence factors. Comparative genome analysis showed the presence in SDSE of the LytSR/LrgAB system and an additional sigma factor (SDEG_0623), both of which were absent from the GAS genome.  Conclusions: These results suggest that the LytSR/LrgAB and CCR play important roles in bacterial resistance to stress microenvironments. Microarray data also indicated that starvation and low oxygen tension partly mimic the microenvironment present during invasive diseases.

sample_organism: Streptococcus dysgalactiae subsp. equisimilis GGS_124

overall_design: To assess the transcriptional responses of SDSE under various stress conditions and to predict in vivo microenvironments during invasive diseases, SDSE was transcriptionally profiled using the SDSE-specific microarray. Logarithmically growing SDSE was exposed to the minimum inhibitory concentrations (MIC) of eight antimicrobial agents (penicillin G, erythromycin, levofloxacin, hydrogen peroxide, sodium nitrite, potassium cyanide, carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and mitomycin) for 30 min. Alternatively, SDSE was exposed to five different growth conditions: stationary phase, nutrient starvation conditions (incubation in phosphate buffered saline (PBS), pH 7.4 for 30 min), exposure to 25 mJ UV, partial pressure of atmospheric carbon dioxide with shaking for 30 min, and anaerobic condition.

first: Tohru

last: Miyoshi-Akiyama


title: OsMOM1 regulated genes in rice: Control transgenic vs OsMOM1a/b double knockdown transgenic

city: Tsukuba

first: Naoki

last: Kishimoto

state: Ibaraki

address: 2-1-2 Kannondai

department: Agrogenomics Research Center

institute: National Institute of Agrobiological Sciences

summary: Transcriptional profiling of young leaves of rice (Oryza sativa) comparing a control transgenic line transformed with p*7GWIWG2(I)-hpt with a double knockdown transgenic line of OsMOM1 genes. Rice has two orthologues (OsMOM1a and OsMOM1b) of Arabidopsis MOM1 gene, which transduces RNA-directed DNA methylation signals to repressive histone modification. To obtain the double knockdown line, at first, single knockdown lines for each OsMOM1 gene were produced with transformation using p*7GWIWG2(I)-hpt-OsMOM1a or p*7GWIWG2(I)-hpt-OsMOM1b. Then a double knockdown plant was selected from progenies of a sexual cross between the single knockdown lines. Both OsMOM1 constructs produce hairpin RNAs and efficiently silence the both target OsMOM1 genes. In the double knockdown line, neither of transcripts from OsMOM1 genes was detected with RNA blot. The double knockdown line might make levels of epigenetic marks (DNA and histone modifications) modified. Goal was to determine the effects of epigenetic change by knockdown of OsMOM1 genes on global gene expression in rice genome.

overall_design: Two-condition experiment, Control transgenic vs. Double knockdown transgenic plants. Biological replicates: 2 control replicates, 2 knockdown replicates.

first: Yoshiki

last: Habu


title: Expression data from Zebrafinch

city: Kyoto

first: Kentaro

last: Abe

state: Kyoto

address: Yoshidakonoe, Sakyo-ku

department: Graduate School of Biostudies, Department of Molecular and Systems Biology

institute: Kyoto University

summary:
The quality of vocal learning is influenced by the tutoring from conspecifics.
We used microarrays to detail the global programme of gene expression underlying differential tutoring condition during the development.

overall_design: Six zebrafinches were reared with or without male tutor form 30-60 days post hatch (dph). At 60 dph, total RNA was extracted from the right forebrain.


title: Global Changes in Gene Expression in Mesorhizobium loti MAFF303099 upon an salt shock

city: Evora

first: Marta

last: Laranjo

address: Apartado 94

department: ICAAM

country: Portugal

institute: Universidade de Evora

summary: Expression profiling of a total of 7281 transcripts was compared between control and salt shock conditions.

overall_design: In the present study, RNA was extracted from three independent cell cultures for each treatment (control and salt shock).

first: Ana

last: Alexandre

first: Solange

last: Oliveira


title: Comparative transcriptomics allows defining mononuclear phagocyte subset homology across vertebrate species (Sheep)

status: Public on Dec 22 2016

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

summary: Characterization of sheep blood and splenic immunocyte subpopulations by means of global expression analysis

overall_design: We analysed the gene expression of blood plasmacytoid dendritic cells (DC) from 3 control sheep, blood SIRPa+ conventional DC (cDC) from 3 control sheep, blood CADM1+ cDC from 1 control sheep, splenic B lymphocytes from 4 control sheep, splenic monocytes/macrophages from 3 control sheep and Monocyte-derived DC from 3 independent in vitro cultures

first: Jamila

last: Elhmouzi-Younes

first: Céline

last: Urien

first: Ruscanu

last: Suzana

first: Luc

last: Jouneau

first: Mickael

last: Bourge

first: Marco

last: Moroldo

first: Gilles

last: Foucras

first: Henri

last: Salmon

first: Hélène

last: Marty

first: Pascale

last: Quéré

first: Nicolas

last: Bertho

first: Pierre

last: Boudinot

first: Marc

last: Dalod

first: Isabelle

last: Schwartz-Cornil


title: Photomixotrophic growth protein A (PmgA) regulates carbohydrate metabolism through the non-coding RNA Ncr0700/PmgR1 in the cyanobacterium Synechocystis sp. PCC 6803

status: Public on Dec 19 2016

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

summary: Carbohydrate metabolism is a tightly regulated process in photosynthetic organisms. The ability to utilize glucose for growth and to regulate storage carbohydrate (i.e. glycogen) metabolisms requires a number of regulatory elements. In the cyanobacterium Synechocystis sp. PCC 6803, the photomixotrophic growth protein A (PmgA), a putative serine/threonine kinase, is involved in governing these abilities; however its downstream regulatory elements are not well studied. Here a genome-wide microarray analysis of a ∆pmgA strain revealed altered transcript levels of several non-coding RNAs, among them Ncr0700 was the most strongly reduced transcript. Generally, Ncr0700 is highly conserved among cyanobacteria. In Synechocystis its expression is light-dependent, i.e. the abundance is reciprocal to the light intensity. Compared to WT and similar to a ΔpmgA mutant, a ∆ncr0700 deletion strain showed a ~2 fold increase in glycogen content under photoautotrophic conditions. Under these conditions ∆ncr0700 grew similarly to the wild type; in contrast its growth was arrested after a shift to photomixotrophic conditions. Ectopic expression of Ncr0700 in ∆ncr0700 as well as ∆pmgA restored both the glycogen and photomixotrophic growth to the wild type levels. These results indicate that Ncr0700 plays a role in regulation of carbohydrate metabolism, acts downstream of PmgA and therefore is renamed here to PmgR1 for photomixotrophic growth RNA 1.

overall_design: We analyzed gene expression in Synechocystis sp. PCC 6803 WT as well as a ∆pmgA (sll1968) mutant grown at 50 μmol photons m–2 s–1 at 30°C with continuous bubbling with air supplemented with 3% (v/v) CO2. Three biological replicates were analyzed for ΔpmgA and compared with 2 replicate cultures of WT.

first: Alice

last: de Porcellinis

first: Lisa

last: Rosgaard

first: Rebekka

last: Kirsch

first: Kirstin

last: Gutekunst

first: Jens

last: Georg

first: Wolfgang

last: Hess

first: Yumiko

last: Sakuragi


title: Gene expression profile of neonate mouse epidermis stem cell after transplacental exposure to Arsenic in drinking water

status: Public on Dec 12 2016

city: Lucknow

first: Shiv

last: Poojan

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

institute: CSIR-Indian Institute of Toxicology Research

summary: Background: The metalloid Arsenic is potentially toxic, genotoxic, and carcinogenic to humans. The metalloid poisining in drinking-water is a widespread problem affecting a large population globally. The toxicant is often found to exceed the recomnded level. the risk of repated exposure is direct as well as transplacental. the primary resion of exposure is the contamination of potable water from the geological sources in many region of the globe. The underlying mechanism of As toxicity is still unknown.

overall_design: Agilent one-color experiment, Organism: Mus musculus , Agilent Custom Mouse Whole Genome Mouse 4x44kk Gene expression designed by Genotypic Technology Private Limited(AMADID: 14868), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Sushil

last: Kumar


title: Effect of erythropoietin (EPO) and leukemia-inhibitory factor (LIF) on miRNA expression profiling in differentiating rat CG4-EPOR oligodendrocytes

status: Public on Dec 08 2016

city: Brighton

first: Pietro

last: Ghezzi

address: BSMS Teaching Building

institute: Brighton & Sussex Medical School

summary: Analysis of the miRNA expression profile in differentiating rat CG4-EPOR oligodendrocytes treated with EPO, LIF or their combination for 1h or 20h

overall_design: miRNA expression was measured in undifferentiated CG4-EPOR cells and in differentiating cells at 1h and 20h in 5 conditions: control, EPO 10ng/ml, LIF 0.2ng/ml, LIF 10ng/ml, EPO 10ng/ml+LIF 10ng/ml); 3 or 4 replicates.

first: Manuela

last: Mengozzi


title: Comparative transcriptomics allows defining mononuclear phagocyte subset homology across vertebrate species

first: Thien-Phong

last: Vu Manh

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

sample_organism:
Sus scrofa
Ovis aries

platform_organism:
Sus scrofa
Ovis aries

overall_design: Refer to individual Series


title: Rational selection of syngeneic preclinical tumor models for immunotherapeutic drug discovery [aCGH]

status: Public on Dec 07 2016

city: Cambridge

first: John

last: Prime

address: Aaron Klug Building

department: Oncology Research

institute: Medimmune

summary: Murine syngeneic tumor models are the cornerstone of novel immuno-oncology (IO)-based therapy development but the molecular and immunological features of these models are still not clearly defined. The translational relevance of differences between the models is not fully understood, impeding appropriate preclinical model selection for target validation, and ultimately hindering drug development. Within a panel of commonly-used murine syngeneic tumor models, we showed variable responsiveness to IO-therapies. We employed aCGH, whole-exome sequencing, exon microarray analysis and flow cytometry to extensively characterise these models and revealed striking differences that may underlie these contrasting response profiles. We identified strong differential gene expression in immune-related pathways and changes in immune cell-specific genes that suggested differences in tumor immune infiltrates between models. We further investigated this using flow cytometry, which showed differences in both the composition and magnitude of the tumor immune infiltrates, identifying models that harbor ‘inflamed’ and ‘non-inflamed’ tumor immune infiltrate phenotypes. Moreover, we found that immunosuppressive cell types predominated in syngeneic mouse tumor models that did not respond to immune-checkpoint blockade, whereas cytotoxic effector immune cells were enriched in responsive models. A cytotoxic cell-rich tumor immune infiltrate has been correlated with increased efficacy of IO-therapy in the clinic and these differences could underlie the varying response profiles to IO-therapy between the syngeneic models. This characterisation highlighted the importance of extensive profiling and will enable investigators to select appropriate models to interrogate the activity of IO-therapies as well as combinations with targeted therapies in vivo.

overall_design: Mouse syngeneic tumour cell lines were grown in vitro n=1 and in vivo n ≈5 subcutaneously on the backs of mice from their parental strain or orthotopically (see sample records for specific details for each mouse model). Mice were sacrificed when tumours reached an average of 200 mm3.  In vitro samples underwent aCGH analysis and transcriptomics analysis while in vivo tumor samples along with a draining lymph node and spleen sample were taken from the same mouse and underwent transcriptomics analysis. Whole exome sequencing and immunophenotyping were also performed on these syngeneic models to in all give a multiomic characterisation of these models.

first: Suzanne

middle: I

last: Mosely

middle: E

first: Richard

last: Sainson

first: Jens-Oliver

last: Koopmann

first: Dennis

middle: Y

last: Wang

first: Danielle

last: Greenawalt

first: Miika

last: Ahdesmaki

first: Rebecca

last: Leyland

first: Stefanie

last: Mullins

first: Luciano

last: Pacelli

last: Marcus

first: Judith

last: Anderton

first: Amanda

last: Watkins

first: Jane

last: Coates Ulrichsen

first: Philip

last: Brohawn

first: Brandon

last: Higgs

first: Matthew

last: McCourt

first: Hazel

last: Jones

first: James

middle: A

last: Harper

first: Michelle

last: Morrow

first: Viia

last: Valge-Archer

first: Ross

last: Stewart

first: Simon

last: Dovedi

first: Robert

middle: W

last: Wilkinson


title: Surface modified titanium dioxide nanoparticles induce fibrosis-like changes in lungs at high doses [set 6]

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

summary: Previous studies have shown that TiO2NPs induce lung inflammation in mice and have suggested that the degree of inflammation varies with their size and other physical and chemical properties, e.g., shapes, surface modifications and surface charge. It is currently unknown if the observed inflammation in mouse lungs following exposure to TiO2NPs will cause any disease in the long term. This study examined mouse lung responses to six individual TiO2NPs of varying sizes (10, 20 and 300 nm), surface modifications and shapes.  C57BL/6 mice were exposed to 18 µg, 54 µg, 162 µg or 486 µg of TiO2NPs/mouse via direct deposition of particles in lungs. Lung fluid and lung tissue were sampled on day 1, day 28 and day 90. Changes in inflammation and gene expression in lung were profiled. Histopathological changes in lungs indicative of diseases were examined by microscopic techniques. The results confirmed that all TiO2NPs induce lung inflammation immediately after exposure. At the highest dose tested, this particular TiO2NPs with surface modification induced signs of lung fibrosis (a disease of regulatory importance for NMs. Although lung response induced by TiO2NPs is influenced by many of their properties, the results of the study indicated that certain surface modification may play role in causing a disease.

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of anatase TiO2NPs of 8 nm diameter. Four different doses were selected: 18, 54, 162, or 486 µg/animal. Samples were collected at day 1, day 28, and day 90 post-exposure

first: Luna

last: Rahman

first: Andrew

last: Williams

first: Dongmei

last: Wu

first: Johnston

last: Michael


title: Surface modified titanium dioxide nanoparticles induce fibrosis-like changes in lungs at high doses [set 5]

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of anatase TiO2NPs of 300 nm diameter. Four different doses were selected:18, 54, 162, or 486 µg/animal. Samples were collected at day 1, day 28, and day 90 post-exposure


title: Comparative transcriptomics allows defining mononuclear phagocyte subset homology across vertebrate species (Pig)

first: Thien-Phong

last: Vu Manh

summary: Characterization of swine blood immunocyte subpopulations by means of global expression analysis

overall_design: We analysed the gene expression of blood plasmacytoid dendritic cells (DC) from 3 control pig, blood SIRPa+ conventional DC (cDC) from 3 control pig, blood CADM1+ cDC from 1 control pig, splenic B lymphocytes from 4 control pig, splenic monocytes/macrophages from 3 control pig and in vitro Monocyte-derived DC from 3 control pig

first: Jamila

last: Elhmouzi-Younes

first: Céline

last: Urien

first: Ruscanu

last: Suzana

first: Luc

last: Jouneau

first: Mickael

last: Bourge

first: Marco

last: Moroldo

first: Gilles

last: Foucras

first: Henri

last: Salmon

first: Hélène

last: Marty

first: Pascale

last: Quéré

first: Nicolas

last: Bertho

first: Pierre

last: Boudinot

first: Marc

last: Dalod

first: Isabelle

last: Schwartz-Cornil


title: Surface modified titanium dioxide nanoparticles induce fibrosis-like changes in lungs at high doses [set 4]

first: Sabina

last: Halappanavar

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of mix rutile/anatase TiO2NPs of 20 nm diameter. Four diferent doses were selected:18, 54, 162, or 486 µg/animal. Samples were collected at day 1, day 28, and day 90 post-exposure

first: Luna

last: Rahman

first: Andrew

last: Williams

first: Dongmei

last: Wu


title: Surface modified titanium dioxide nanoparticles induce fibrosis-like changes in lungs at high doses [set 3]

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of rutile hydrophobic TiO2NPs of 20 nm diameter. Four different doses were selected:18, 54, 162, or 486 µg/animal. Samples were collected at day 1, day 28, and day 90 post-exposure

first: Johnston

last: Michael


title: Surface modified titanium dioxide nanoparticles induce fibrosis-like changes in lungs at high doses [set 2]

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of rutile hydrophilic TiO2NPs of 20 nm diameter. Four different doses were selected:18, 54, 162, or 486 µg/animal. Samples were collected at day 1, day 28, and day 90 post-exposure


title: Surface modified titanium dioxide nanoparticles induce fibrosis-like changes in lungs at high doses [set 1]

overall_design: This experiment examined the the lung transcriptomic responses to single intratracheal instillation of anatase TiO2NPs of 20 nm diameter. Four different doses were selected:18, 54, 162, or 486 µg/animal. Samples were collected at day 1, day 28, and day 90 post-exposure


title: Surface modified titanium dioxide nanoparticles induce fibrosis-like changes in lungs at high doses


title: The histone deacetylase inhibitor Suberoylanilide Hydroxamic Acid (SAHA) alleviates salinity stress in cassava (Manihot esculenta Crantz)

status: Public on Dec 01 2016

city: Phayathai

first: Onsaya

last: Patanun

state: Bangkok

address: Rama6 rd. Phayathai

department: Biotechnology

country: Thailand

institute: Mahidol university

summary: To elucidate the molecular mechanism involved in increased tolerance to high-salinity stress by the application of HDAC inhibitor named SAHA

overall_design: Cassava cultivar TMS6044 was asexually propagated in a plastic pot with MS medium. The 5-cm length shoot top of 3-month-old cassava plantlets were cut and then transferred to liquid MS media without agar. After one week incubation, the plantlets showing root elongation were treated with 100 µM SAHA for 24 h, followed by treatment with 200 mM NaCl for 2 and 24 h. 100 ng of total RNA were used.

first: Minoru

last: Ueda

first: Misao

last: Itouga

first: Yoshinori

last: Utsumi

first: Akihiro

last: Matsui

first: Maho

last: Tanaka

first: Chikako

first: Hitoshi

last: Sakakibara

last: Yoshida

first: Jarunya

last: Narangajavana

first: Motoaki

last: Seki


title: Gene expression profile of EBF1-wt & EBF1-H240A

status: Public on Nov 21 2016

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: To study the function of EBF1-H240 residue, a gain-of function microarray analysis was performed by transducing Empty, Ebf1-wt and Ebf1-H240A expressing vectors into Ebf1-/- progenitor cells.

overall_design: Freshly prepared Ebf1−/− c-Kit+ fetal liver cells were transduced with pmys-Empty-IRES-GFP, pmys-EBF1wt-IRES-GFP or pmys-EBF1H240A-IRES-GFP. The GFP positive transduced cells were sorted 36 hrs after transduction.

first: Cheng-Yuan

last: Yang


title: The isopeptidase inhibitor 2cPE triggers proteotoxic stress and ATM activation in chronic lymphocytic leukemia cells.

status: Public on Oct 31 2016

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

country: Italy

institute: university of Udine

summary: In this study we investigated changes in gene expression induced by 2cPE (a non-selective isopeptidase inhibitor) in leukemia cells isolated from 10 different patients suffering of B-cell chronic lymphocytic leukemia. We compared 2cPE induced changes in mRNA levels with those induced by bortezomib, another well characterized proteasome inhibitor. Both inhibitors trigger apoptosis in leukemia cells.

overall_design: Gene expression profiles of B-CLL cells coming from several patients treated with the UPS inhibitors bortezomib and 2cPE are compared to the profiles of untreated cells.

first: Andrea

last: Tomasella

first: Raffaella

last: Picco

last: Agorbissa

first: Elisa

last: Bianchi

first: Rossella

last: Manfredini

first: Fabio

last: Benedetti

first: Trimarco

last: Valentina

first: Federica

last: Frezzato

first: Livio

last: Trentin

first: Gianpiero

last: Sememzato

first: Domenico

last: Delia

first: Claudio

last: Brancolini


title: Fat-specific protein 27/CIDEC plays an important role in promoting alcoholic liver injury in mice and humans

city: Rockville

first: Ming-Jiang

last: Xu

state: MD

address: 5625 Fishers LN, 2S12

department: NIAAA

country: USA

institute: NIH

summary: Here, we developed a mouse model with long-term chronic (8-12 week) plus single/multiple binge ethanol feeding, which mimicks the drinking patterns of AH patients, who often have a history of chronic drinking plus recent excessive drinking. This model produces severe macrosteatosis, significant inflammation, and mild fibrosis. Moreover, we conducted translational studies by comparing transcriptome data from this clinically relevant in vivo model and human AH biopsy samples, and identified many similar disregulated genes in this animal model and AH samples. And we find that FSP27/CIDE-C plays a critical role in promoting steatosis and hepatocellular damage in mouse and in human AH.

overall_design: Six-condition experiment, P8w, P10d, E8w, E10d1B, E8w1B,E8wMB

first: Ming

first: Yan

last: Cai

first: Bin

last: Gao


title: HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_human_Fibs_1]

status: Public on Oct 20 2016

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: HnRNPA2B1 encodes an RNA binding protein associated with neurodegenerative disorders. However, its function in the nervous system is unclear. Transcriptome-wide cross-linking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ~2,500 hnRNP A2/B1 binding sites and an unexpected role for hnRNP A2/B1 in alternative polyadenylation. Loss of hnRNP A2/B1 results in alternative splicing, including skipping of an exon in amyotrophic lateral sclerosis (ALS)-associated D-amino acid oxidase (DAO) that reduces D-serine metabolism. Inclusion of the DAO exon is also reduced in transgenic ALS mice models. ALS-associated hnRNP A2/B1 D290V mutant patient fibroblasts and motor neurons differentiated from induced pluripotent stem cells demonstrate gain-of-mutant-dependent splicing differences. Mutant motor neurons also exhibit increased hnRNP A2/B1 localization to cytoplasmic granules during stress, which are abrogated by a small molecule CA43.  Our findings and cellular resource identify RNA networks affected in loss of normal and mutated hnRNP A2/B1 with broad relevance to neurodegeneration.

overall_design: Microarray in human primary fibroblasts treated with ASO to deplete hnRNP A2/B1 and controls. Three replicates per condition.

first: Fernando

last: Martinez

first: Gabriel

last: Pratt

first: Eric

last: Van Nostrand

first: Ranjan

last: Batra

first: Stephanie

last: Huelga

first: Katannya

last: Kapeli

first: Peter

last: Freese

first: Seung

last: Chun

first: Karen

last: Ling

first: Chelsea

last: Gelboin-Burkhart

first: Layla

last: Fijany

first: Harrison

last: Wang

first: Julia

middle: K

last: Nussbacher

first: Hong-joo

last: Kim

first: Rea

last: Lardelli

first: Balaji

last: Sundararaman

first: John

middle: P

last: Donohue

first: Jens

last: Lykke-Andersen

first: Frank

last: Bennett

first: Manuel

last: Ares Jr

first: Christopher

last: Burge

first: J

last: Taylor

last: Rigo


title: Engineering of Three Dimensional Micro Nerve Tissue Using Postnatal Stem Cells from Human Dental Apical Papilla

status: Public on Nov 01 2016

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

summary: The generation of cell-based three dimensional (3D) nerve tissue is an attractive subject to improve graft survival and integration into host tissue for neural tissue regeneration or to model biological events in stem cell differentiation. However, although 3D organotypic culture strategy has been well established for 3D nerve tissue formation of pluripotent stem cells to study underlying biology in nerve development, cell-based nerve tissue have not been developed using human postnatal stem cells with therapeutic potential of stem cell-based therapy. Here, we established culture strategy for the generation of in vitro cell-based 3D nerve tissue from postnatal stem cells from apical papilla (SCAPs) of tooth, which is known to be originated from neural crest-derived ectomesenchyme. A stem cell population capable of differentiating into neural cell lineages was generated during the ex-vivo expansion of SCAPs in the presence of EGF and bFGF, and SCAPs differentiated into neural cells showing neural cell lineage-related molecular and gene expression profiles with morphological change under neural inductive culture condition. Moreover, we showed the first evidence that 3D cell-based nerve-like tissue with axon and myelin structure could be generated from SCAPs via 3D organotypic culture using an integrated bioprocess composing of polyethylene glycol (PEG) microwell-mediated cell spheroid formation and subsequent dynamic culture in a high aspect ratio vessel (HARV) bioreactor. In conclusion, our study propose that the culture strategy provide a novel approach to develop in vitro engineered nerve tissue using SCAPs and a foundation to study biological events in neural differentiation of postnatal stem cells.

overall_design: For DNA microarray analysis of the ex-vivo expanded stem cells derived from apical papillas, RNA was extracted from the ex-vivo expanded SCAPs at passage of 3, 6 and 9.

first: Yu-Shik

last: Hwang

first: Byung-Chul

first: Sung-Min

last: Jun

first: So Yeon

first: Yong-Dae

last: Kwon

first: Sung Chul

last: Choe

first: Eun-Chul

first: Jinseok

first: Jun-Kyo

middle: F

last: Suh


title: Mature IgM+ plasma cells sense antigen and develop competence for cytokine production upon antigenic challenge

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

institute: AltraBio

summary: Dogma holds that plasma cells (PC), as opposed to B cells, cannot bind antigen (Ag) because they have switched from expression of membrane-bound immunoglobulins that constitute the B cell Ag receptor (BCR) to production of the secreted form of immunoglobulins. We have compared the phenotypical and functional attributes of PC generated by the T-cell-dependent and T-cell-independent forms of the hapten NP. We unexpectedly found that the nature of the secreted Ig isotype rather than the chemical structure of the immunizing Ag defines two functionally distinct populations of PC. Fully mature IgM-expressing bone marrow PC retain expression of a functional BCR while their IgG+ counterparts do not. We show that Ag boost modifies the gene expression profile of IgM+ PC and initiates a cytokine production program, characterized by upregulation of CCL5 and IL-10. Our results demonstrate that IgM-expressing PC can sense Ag and acquire competence for cytokine production upon antigenic challenge.

overall_design: Two experimental groups (control and boost) composed of 5 distinct samples each

first: Pascal

last: BLANC P

first: Ludovic

last: MORO-SIBILOT

first: Ferdinand

last: JAGOT

last: de BERNARD

first: Laurent

last: BUFFAT

first: Sébastien

last: DUSSURGEY

first: Elias

last: HOBEIKA

first: Morgan

last: TAILLARDET

first: Olivier

last: THAUNAT

first: Antoine

last: SICARD

first: Paul

last: MONDIERE

last: GENESTIER

first: Stephen

middle: L

last: NUTT

first: Thierry

last: DEFRANCE


title: The effects of bifenthrin on the transcriptome of a euryhaline fish

city: Davis

first: Ken

last: Jeffries

address: One Shields Avenue

institute: UC Davis

summary: Bifenthrin is a commonly detected pesticide in California surfacewaters; however the effects of bifenthrin on aquatic organisms are complex and poorly understood. This study presents the transcriptome-wide response of the inland silverside, Menidia beryllina, to chronic 14 d exposures to bifenthrin.

overall_design: Twenty-three samples were run on 23 arrays, there were 4-7 replicates for each of three bifenthrin exposure concentrations and a control group.

first: Bryan

last: Cole

first: Susanne

last: Brander

first: Richard

last: Connon


title: Gene expression data of human mesenchymal stromal cells, fibroblasts and hematopoietic progenitors

status: Public on Oct 21 2016

city: Salamanca

first: Beatriz

middle: Roson

last: Burgo

address: Campus Miguel de Unamuno

department: Cancer Research Centre

institute: Consejo Superior de Investigaciones Científicas & Universidad de Salamanca

summary: The data presented is intended to analyse the changes in the expression profiles of human MSCs (Mesenchymal Stromal/Stem Cells) associated to different tissue specific stimulus.

overall_design: Human BM-, PL-, and AD- MSCs, and skin fibroblasts from healthy independent donors were isolated and expanded in vitro. Hematopoietic progenitors and stem cells (HSCs) were isolated applying CD34+ immunomagnetic selection.

last: Roson-Burgo

first: Fermin

last: Sanchez-Guijo

first: Consuelo

last: Del Cañizo

first: Javier

last: De Las Rivas


title: Gene expression profiling in MCF7 cell lines under hypoxia and reoxygenation

city: Maastricht

first: Michiel

last: Adriaens

address: Universiteitssingel 60

department: Maastricht Centre for Systems Biology - MaCSBio

country: Netherlands

institute: Maastricht University

summary:
Purpose: Study hypoxia and reoxygenation induced changes in genome-wide gene expression
Methods: Using the MCF7 breast epithelial adenocarcinoma cell line as a model, we studied epigenomic reprogramming as a function of fluctuating oxygen tension. To this end, we performed a transcriptomics analysis in MCF7 cells subjected to changes in oxygenation (i.e. acute hypoxia, chronic hypoxia, reoxygenation).
Results: Global downregulation upon hypoxia; partial restore on reoxygenation.
Conclusions: Our data show that oxygen availability dynamically regulates gene transcription.

overall_design: Genome-wide transcriptomics analysis was performed on the Affymetrix Hugene STv1 microarray platform.

first: Peggy

last: Prickaerts

first: Willem

last: Voncken

first: Brad

last: Wouters


title: Comparison of microRNA profiles between Normoxia and Hypoxia

city: HOUSTON

first: anil

middle: k

last: sood

state: TEXAS

address: 7777 knight road, unit 173

department: Gyn Oncology and Rep Medicine

institute: UT MD Anderson Cancer Center

summary: We used miRNA array to study differential expression of miRNA under hypoxia exposure in cancer cells. Cells cultured under normoxia were used as controls.

overall_design: Hypoxia induced differential expression in miRNAs were meassured by treating epithelial ovarian cancer cell line A2780 at 1% O2 for 6hr, 48hr and 6days. Cells not treated with hypoxia (21% O2) were used as control.

first: Anil

last: Sood

first: Rajesha

last: Rupaimoole


title: Expression profiling in primary embryonic fibroblasts deficient for the lats2 locus

status: Public on Oct 16 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: We previously reported LATS2 null mice (Yabuta et al., 2007). LATS2 known as a tumor suppressor protein. However, the LATS2 mediated transcriptional regulation remains largely unknown. To investigate potential signaling pathways, we performed the expression profiling by using primary MEFs derived from wild type and LATS2 null mice.

overall_design: Total RNAs were extracted from MEFs derived from LATS2+/+ and LATS2-/- C57BL/6J mice using miRNeasy extraction kit (Qiagen). A Dye-swapped experiment was performed by hybridizing complimentary RNA (cRNA) labeled with either Cyanine (Cy) -3 or Cy-5 (Perkin-Elmer) onto Whole Mouse Genome Oligo Microarray (G4122F; Agilent Technologies).

first: Hiroshi

last: Nojima


title: Raw microarray derived data for evaluation of a feature and template-assisted assembler for the analysis of foot-and-mouth disease virus by sequence assembly

status: Public on Nov 10 2016

city: Greenport

first: Roger

middle: William

last: Barrette

state: NY

address: Plum Island Animal Disease Center

department: Diagnostic Services

institute: USDA/APHIS/FADDL

summary: Here we describe a custom FMDV microarray and a companion feature and template-assisted assembler software (FAT-assembler) capable of resolving virus genome sequence using a moderate number of conserved microarray features.  The results demonstrate that this approach may be used to rapidly characterize naturally occurring FMDV as well as an engineered chimeric strain of FMDV.  The FAT-assembler, while applied to resolving FMDV genomes, represents a new bioinformatics approach that should be broadly applicable to interpreting microarray genotyping data for other viruses or target organisms

overall_design: Seven field isolates of Foot-and-Mouth Disease virus,  representing each of seven serotypes, as well as a single chimeric strain were subject to total nucleic acid extraction, and subsequent nucleic acid amplification, and fluorescent labeling.  Labeled nucleic acid was hybridized to Agilent (8x60K) custom microarrays (Agilent-033126) and scanned using GenePix software.  The output of the raw GPR file was then passed through the feature and template assisted assembler software for producing consensus sequence which was then compared to the known sequence for determination of accuracy of the algorithm.

first: R

first: J

last: Rowland

first: F

middle: J

last: Grau

first: M

last: McIntosh


title: HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_human_iPSC_MN_ASO]

first: Gene

last: Yeo

overall_design: Microarray in human iPSC-MNs from patients with hnRNP A2/B1 D290V mutations or controls. Samples treated with ASO againnst hnRNP A2/B1 or nontargetting ASO. 3 replicates per condition

first: Fernando

last: Martinez

first: Gabriel

last: Pratt

first: Eric

last: Van Nostrand

first: Ranjan

last: Batra

first: Stephanie

middle: C

last: Huelga

first: Katannya

last: Kapeli

first: Peter

last: Freese

first: Seung

last: Chun

first: Karen

last: Ling

first: Chelsea

last: Gelboin-Burkhart

first: Layla

last: Fijany

first: Harrison

last: Wang

first: Julia

last: Nussbacher

first: Hong-joo

last: Kim

first: Rea

last: Lardelli

first: Balaji

last: Sundararaman

first: John

last: Donohue

first: Jens

last: Lykke-Andersen

first: Frank

last: Bennett

first: Manuel

last: Ares Jr

first: Christopher

middle: B

last: Burge

last: Taylor

last: Rigo


title: De Novo Copy Number Variations (CNVs) in ESC Derived from Intact and ST Blastocysts

status: Public on Oct 14 2016

city: Cincinnati

first: Shiyu

last: Luo

state: OH

address: 3333 Burnet Ave

institute: CCHMC

summary: Because ST embryos may be at risk of procedure related chromosomal or sub-chromosomal abnormalities, we biopsied and examined expanded blastocysts derived from ST and control embryos. We examined copy number variations (CNVs) by SNP array to explore possible subchromosomal abnormalities (deletion or duplication) in selected ST ESCs. De novo CNVs were detected in both ST and intact controls but none carried clinical significance (Table S3 in the Supplementary Appendix).

overall_design: A total of twelve ESC lines were examined by microarray analysis using the Infinium Assay with the Illumina CytoSNP-850Kv1.1 BeadChip platform. This chip contains approximately 843,390 genome-wide markers, an overall average probe spacing of 1.8 kb and an average effective resolution of 18 kb to determine copy number change.

first: Taosheng

last: Huang

first: Xinjian


title: DNA Methylation Patterns in Rat Mammary Carcinomas Induced by Pre- and Post-Pubertal Irradiation

status: Public on Oct 11 2016

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

summary: Several lines of evidence indicate one's age at exposure to radiation strongly modifies the risk of radiation-induced breast cancer. We previously reported that rat mammary carcinomas induced by pre- and post-pubertal irradiation have distinct gene expression patterns, but the changes underlying these differences have not yet been characterized. The aim of this investigation was to see if differences in CpG DNA methylation were responsible for the differences in gene expression between age at exposure groups observed in our previous study.

overall_design: DNA was obtained from the mammary carcinomas arising in female Sprague-Dawley rats that were either untreated or irradiated (γ-rays, 2 Gy) during the pre- or post-pubertal period (3 or 7 weeks old). The DNA methylation was analyzed using CpG island microarrays and the results compared to the gene expression data from the original study.

first: Masaru

last: Takabatake

first: Benjamin

last: Blyth

last: Daino

first: Tatsuhiko

last: Imaoka

first: Mayumi

last: Nishimura

first: Masahiro

last: Fukushi

first: Yoshiya

last: Shimada


title: Ubiquitin proteasome expression in Mulitple Myeloma cell lines

city: Belfast

first: Lisa

last: Crawford

address: 97 Lisburn Road

department: CCRCB

institute: Queen's University Belfast

summary: The ubiquitin proteasome system plays an important role in the pathophysiology of Multiple Myeloma, highlighted by the unique success of proteasome inhibitors in this malignancy. Using topic-defined microarrays we have looked at expression of ubiquitin proteasome system genes in 2 multiple myeloma cell lines and normal bone marrow samples.

overall_design: Normal bone marrow samples from 5 healthy donors and 2 multiple myeloma cell lines, OPM-2 (4 replicates) and U266 (3 replicates), were included in the study.


title: 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) increase CREB1 binding to the C/EBP half-site GCAA

status: Public on Oct 19 2016

city: Bethesda

first: Desiree

last: Tillo

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: In human and mouse stem cells and brain, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) can occur outside of CG dinucleotides.  Using protein binding microarrays (PBMs) containing 60-mer DNA probes, we evaluated the effect of 5mC and 5hmC on one DNA strand on the double-stranded DNA binding of the mouse B-ZIP transcription factors (TFs) CREB1, ATF1, and JUND.  5mC inhibited CREB1 binding to the canonical CRE half-site |GTCA, but increased binding to the C/EBP half-site |GCAA.  5hmC inhibited CREB1 binding to all 8-mers except TGAT|GCAA, where binding is enhanced.  We observed similar DNA binding patterns with the closely related TF: ATF1.  In contrast, both 5mC and 5hmC inhibited binding of JUND.  These results identify new DNA sequences that are well-bound by CREB1 and ATF1 only when they contain 5mC or 5hmC.  Analysis of two x-ray structures examines the consequences of 5mC and 5hmC on DNA binding by CREB and FOS|JUN.

overall_design: Protein binding microarray (PBM) experiments were performed for a set of 3 mouse B-ZIP transcription factors, CREB1, ATF1, and JUND. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded 44K Agilent microarrays (Berger et al., Nature Biotechnology 2006) in order to determine their binding preferences to sequences containing modified cytosines.  We modified the double stranding step of the PBM protocol in which the nucleotide mixture contained 5-methylcytosine or 5-hydroxymethylcytosine.  Details of the modified cytosine PBM protocol are described in Khund-Sayeed S et al., Integrative Biology, 2016.


title: Microarray gene expression analysis in ovine ductus arteriosus during fetal development and birth transition.

status: Public on Oct 12 2016

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

summary: Patent ductus arteriosus (PDA) in the newborn is the most common congenital heart anomaly, and is significantly more common in preterm infants. Contemporary pharmacological treatment is effective in only 70 to 80% of the cases. Moreover, indomethacin or ibuprofen, which are used to close a PDA may be accompanied by serious side effects in premature infants. To explore the novel molecular pathways, which may be involved in the maturation and closure of the ductus arteriosus (DA), we used fetal and neonatal sheep to test the hypothesis that maturational development of DA is associated with significant alterations in specific mRNA expression.

overall_design: We isolated DA and a segment of ascending aorta from preterm (97±0 days gestation) and near-term (136 ± 0.8 days) fetal sheep (full term = 145 days) and from 12±0 hours old newborn lambs (obtained from Pozzi Ranch, Valley Ford, CA)). Four animals (n=4) were used for each experimental group. At the time of experimental study, ewes and newborn lambs were euthanized with an overdose of the proprietary euthanasia solution Euthasol (pentobarbital sodium 100 mg.Kg-1 and phenytoin sodium 10 mg.Kg-1; Virbac, Ft. Worth, TX).


title: Genome-wide ChIP-chip Rad50 in early S-phase in the presence of hydroxyurea

status: Public on Oct 18 2016

city: Basel

first: Jérôme

last: Poli

address: 66 Maulbeerstrasse

department: Quantitative Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Genome binding/occupancy profiling by genome tiling array

summary:
The Mre11-Rad50-Xrs2 (MRX) complex is related to SMC complexes that form rings capable of holding two distinct DNA strands together. MRX functions at stalled replication forks and double-strand breaks (DSB). A mutation in the N-terminal OB-fold of the 70-kD subunit of yeast replication protein A, rfa1-t11, abrogates MRX recruitment to both types of damage. The rfa1 mutation is functionally epistatic with loss of any of the MRX subunits for survival of replication fork stress or DSB recovery, although it does not compromise end resection. High resolution imaging shows that either the rfa1-t11 or the rad50 mutation lets stalled replication forks collapse, and allows the separation not only of opposing ends, but of sister chromatids at breaks. Given that cohesin loss does not provoke visible sister separation as long as the RPA -MRX contacts are intact, we conclude that MRX also serves as a structural lynchpin of sister chromatids at breaks.
Rad50 is a member of the Mre11-Rad50-Xrs2 (MRX) complex which is known to associate to replication forks under hydroxyurea-stress condition. Using ChIP-chip, we show that MRX recruitment to replication forks partially rely on Rfa1 (RPA) at the genome-wide level.

overall_design: Rad50-ChIP from wild-type cells and rfa1-t11 (25°C)

first: Andrew

last: Seeber

first: Anna

last: Hegnauer

first: Nicole

last: Hustedt

first: Ishan

last: Desphande

first: Jan

last: Eglinger

first: Philippe

last: Pasero

first: Heinz

last: Gut

first: Miki

last: Shinohara

first: Karl-Peter

last: Hopfner

first: Kenji

first: Susan

middle: M

last: Gasser


title: HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_human_Fibs_2]

first: Gene

last: Yeo

overall_design: Microarray in human primary fibroblasts from patients with MSP and controls two conrols, two hnRNP A2/B1 D290V patients, and one VCP R155H patient. Three replicates per condition.

first: Fernando

last: Martinez

first: Gabriel

last: Pratt

first: Eric

last: Van Nostrand

first: Ranjan

last: Batra

first: Stephanie

last: Huelga

first: Katannya

last: Kapeli

first: Peter

last: Freese

first: Seung

last: Chun

first: Karen

last: Ling

first: Chelsea

last: Gelboin-Burkhart

first: Layla

last: Fijany

first: Harrison

last: Wang

first: Julia

last: Nussbacher

first: Hong-joo

last: Kim

first: Rea

last: Lardelli

first: Balaji

last: Sundararaman

first: John

last: Donohue

first: Jens

last: Lykke-Andersen

first: Frank

last: Bennett

first: Manuel

last: Ares Jr

first: Christopher

last: Burge

first: J

last: Taylor

last: Rigo


title: Differentially expressed genes between non-treated and salt-treated WT plants

status: Public on Oct 07 2016

city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

institute: Pusan National University

summary: The experiment was designed to identify differentially expressed genes between control and NaCl-treated WT seedlings

overall_design: Arabidopsis Columbia WT seedlings (14-day-old, short-day condition), 300 mM NaCl treatment for 0h, 2h, 5h, 2 biological replicates

first: Hye-Yeon

last: Seok

first: Dong-Hyuk

last: Woo


title: Bach2 inhibits Th2-type immune responses by regulating glutamine metabolism [expression array]

status: Public on Nov 14 2016

city: Toon-shi

first: Makoto

last: Kuwahara

state: Ehime

address: Shitsukawa

department: Department of Immunology

institute: Graduate School of Medicine, Ehime University

summary: It is becoming clear that the acquisition of T cell functions is closely linked to the reprogramming of the metabolic pathway.  However, the impact of metabolic changes on the differentiation of helper T cell subsets remains unclear.  We herein demonstrate a critical role of glutamine metabolism in regulating type 2-immune response.  Bach2, a transcriptional repressor, binds to an AP-1 motif, and suppresses Th2 cell differentiation and glutaminolysis.  Glutaminase 2, which controls glutamine metabolism, was identified as a Bach2 target gene.  The pharmacological inhibition of glutamine metabolism normalized allergic lung inflammation that developed spontaneously in T-cell specific Bach2-deficient mice.  These findings reveal the importance of the Bach2-dependent modulation of glutamine metabolism in regulating Th2 cell differentiation and Th2 cell- mediated inflammation.

overall_design: Gene expression in Bach2 WT-Th (Bach2 WT-Th (-)), Bach2 KO-Th (Bach2 KO-Th (-)), restimulated Bach2 WT-Th (Bach2 WT Th (+)) and re-stimulated Bach2 KO-Th (Bach2 KO Th (+)).

first: Maya

last: Izumoto

first: Junpei

last: Suzuki

first: Mizuki

last: Ochi

first: Kanta

last: Shioiri

first: Akira

last: Matsumoto

first: Takeshi

last: Yamada

first: Kenta

last: Shinoda

first: Toshinori

last: Nakayama

first: Tomohiro

last: Kurosaki

first: Tatsuya

last: Sawazaki

first: Osamu

last: Ohara

first: Masaki

last: Yasukawa

first: Masakatsu

last: Yamashita


title: Mechanisms for Complex Chromosomal Insertions

status: Public on Oct 30 2016

city: Houston

first: Shen

last: Gu

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics Laboratories using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing to glean insights into potential mechanisms of formation.

overall_design: Seven individuals with complex chromosomal insertions were subjected to custom high-density arrays in the targeted regions.


title: Beta-adrenergic-activated macrophages: Location in the M1-M2 spectrum and transcriptional regulation

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

institute: UCLA

summary: Genome-wide transcriptional profiling results were used to systematically assess the extent to which transcriptomes of beta-adrenergic-activated macrophages show expression of genes that are characteristic of the canonical IL-4-stimulated M2 macrophage vs. IFN-gamma-stimulated M1 macrophage and to infer potential transcriptional regulators.

overall_design: Total RNA obtained from bone marrow derived macrophages (BMDMs) of Balb/c female mice (aged 8-10 weeks) incubated with isoproterenol, IL-4, IFN-gamma, or only media for 24 hours.  Transcript origin analysis was used to assess the relative polarity of BMDMs activated by isoproterenol, using IL-4-activated and IFN-gamma-activated BMDMs as reference.  TELiS used to assess potential transcriptional regulation.


title: Multi-parametric profiling of non-small cell lung cancers reveals distinct immunophenotypes [Nanostring]

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

summary:
Background: Immune checkpoint blockade improves survival in a subset of patients with non-small cell lung cancer (NSCLC), but robust biomarkers that predict response to PD-1 pathway inhibitors are lacking.  Furthermore, our understanding of the diversity of the NSCLC tumor immune microenvironment remains limited.    Methods: We performed comprehensive flow-cytometric immunoprofiling on both tumor and immune cells from 51 NSCLCs and integrated this analysis with clinical and histopathologic characteristics, next generation sequencing, mRNA expression, and PD-L1 immunohistochemistry (IHC).    Results:  Cytometric profiling identified an immunologically “hot” cluster with abundant CD8+ T cells expressing high levels of the PD-1 and TIM-3, and an immunologically “cold” cluster with lower relative abundance of CD8+ T cells and expression of inhibitory markers.  The “hot” cluster was highly enriched for expression of genes associated with T cell trafficking and cytotoxic function, and high PD-L1 expression by IHC.  There was no correlation between immunophenotype and KRAS or EGFR mutation, or patient smoking history, but we did observe an enrichment of squamous subtype and tumors with higher mutation burden in the “hot” cluster.  Additionally, ~20% of cases had high B cell infiltrates with a subset producing IL-10.    Conclusions: Our results support the use of immune-based metrics to study response and resistance to immunotherapy in lung cancer.   Background: Immune checkpoint blockade improves survival in a subset of patients with non-small cell lung cancer (NSCLC), but robust biomarkers that predict response to PD-1 pathway inhibitors are lacking.  Furthermore, our understanding of the diversity of the NSCLC tumor immune microenvironment remains limited.    Methods: We performed comprehensive flow-cytometric immunoprofiling on both tumor and immune cells from 51 NSCLCs and integrated this analysis with clinical and histopathologic characteristics, next generation sequencing, mRNA expression, and PD-L1 immunohistochemistry (IHC).    Results:  Cytometric profiling identified an immunologically “hot” cluster with abundant CD8+ T cells expressing high levels of the PD-1 and TIM-3, and an immunologically “cold” cluster with lower relative abundance of CD8+ T cells and expression of inhibitory markers.  The “hot” cluster was highly enriched for expression of genes associated with T cell trafficking and cytotoxic function, and high PD-L1 expression by IHC.  There was no correlation between immunophenotype and KRAS or EGFR mutation, or patient smoking history, but we did observe an enrichment of squamous subtype and tumors with higher mutation burden in the “hot” cluster.  Additionally, ~20% of cases had high B cell infiltrates with a subset producing IL-10.    Conclusions: Our results support the use of immune-based metrics to study response and resistance to immunotherapy in lung cancer.
29 NSCLC cases analyzed wth Nanostring human PanCancer immune module

overall_design: 29 cases

first: Patrick

last: Lizotte

first: Elena

last: Ivanova


title: VRS2 regulates hormone-mediated inflorescence patterning in barley

city: Los Banos

last: Sreenivasulu

address: Metro Manila

country: Philippines

institute: IRRI

summary: In the present study, we elucidate the molecular and hormonal role of the Six-rowed spike 2 (Vrs2) — a SHORT INTERNODES (SHI) transcriptional regulator during barley inflorescence and shoot development. Here we show that Vrs2 is specifically involved in floral organ patterning and phase duration by maintaining hormonal homeostasis and gradients during normal spike development; but similarly influenced plant stature traits. Furthermore, we establish a first link between the SHI-protein family and sucrose metabolism during organ growth and development, which may have implications for deeper molecular insights into crops' inflorescence and plant architecture. Differential gene expression study between BW-NIL(vrs2.e) vs. Bowman was done on the extracted RNA from immature shoot apices to infer the differences at level of expression at early spike developmental stages (triple mound (TM), glume primordia (GP), stamen primordia (SP), awn primordia (AP)).

overall_design: For microarray study, the immature shoot apices collected from BW-NIL(vrs2.e) and WT progenitor Bowman at AP, GP, SP and TM were used. The RNA from these tissues was extracted using Plant Mini RNA kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. The quantity of RNA was measured using the NanoDrop ND-1000 (Peqlab, Erlangen, Germany). The quality of the extracted RNA was verified with a Bioanalyzer 2100 device (Agilent Technologies, Santa Clara, CA, USA). The RNA was labeled through the application of a Low Input Quick Amp Labeling kit (Agilent Technologies). The labeled cRNA samples were subsequently purified using RNeasy mini spin columns (Qiagen) and 600ng of Cy3-labeled, amplified cRNA were hybridized, following the manufacturer's protocol, to a custom-synthesized 60k Barley Microarray (Agilent Technologies).

first: Helmy

last: Youssef

first: Kai

last: Eggert

first: Ravi

last: Koppolu

first: Ahmad

last: Alqudah

first: Naser

last: Poursarebani

first: Arash

last: Fazeli

first: Shun

last: Sakuma

first: Akemi

last: Tagiri

first: Twan

last: Rutten

first: Geetha

last: Govind

first: Udda

last: Lundqvist

first: Andreas

last: Graner

first: Takao

last: Komatsuda

first: Nese

first: Thorsten

last: Schnurbusch


title: A Putative Blood-Based Biomarker for Autism Spectrum Disorder-Associated Ileocolitis

city: Winston Salem

first: Stephen

last: Walker

address: Medical Center Blvd

institute: Wake Forest University Health Sciences

summary: Analysis of gene expression in inflamed gastrointestinal tissue and blood from GI-symptomatic children with ASD compared to non-inflamed tissue and blood from typically developing GI-syptomatic children. The hypothesis being tested was that peripheral blood would yield a surrogate biomarker for GI inflammation in children with ASD.

overall_design: Total RNA was isolated from inflamed gastrointestinal tissue (terminal ileum and/or colon) and peripheral blood from children with ASD and corresponding (non-iflamed) tissue and blood from typically developing children.

first: Arthur

last: Krigsman


title: miR-338-3p controls the late onset of auditory thalamocortical disruption in schizophrenia models

status: Public on Oct 10 2016

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Among the fundamental unresolved questions in psychiatry is why symptoms of psychosis, such as auditory hallucinations in schizophrenia, fail to appear until early adulthood. Here we report that in mouse models of 22q11.2 deletion syndrome (22q11DS), a leading genetic cause of schizophrenia, synaptic transmission at thalamocortical inputs to the auditory cortex becomes disrupted later in life, thereby recapitulating the adult onset of psychosis. Age-dependent disruption of thalamocortical synaptic transmission in 22q11DS is mediated by dopamine receptor Drd2-targeting microRNA miR-338-3p, which is enriched in the thalamus but becomes depleted due to haploinsufficiency of the microRNA-processing 22q11DS gene Dgcr8. Deletion/knockdown of miR-338-3p causes the Drd2 increase in the auditory thalamus and abnormal sensitivity of 22q11DS thalamocortical inputs to antipsychotics, replicates auditory synaptic and behavioral abnormalities in 22q11DS, and eliminates age dependence of these auditory deficits. These results suggest that miR-338-3p mediates the pathogenic mechanism of 22q11DS-related psychosis and controls its late onset.

overall_design: Profile the miRNA expression changes between wild type and mutant (Df(16)1/+, Dgcr8+/-)  mice.

first: Sungkun

last: Chun

first: Fei

last: Du

first: Joby

last: Westmoreland

first: Yong

middle: D

first: Donnie

last: Eddins

first: Ildar

middle: T

last: Bayazitov

first: Prakash

last: Devaraju

first: Marcia

last: Mellado Lagarde

first: Stanislav

middle: S

last: Zakharenko


title: HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_mouse_SC]

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: HnRNPA2B1 encodes an RNA binding protein associated with neurodegenerative disorders. However, its function in the nervous system is unclear. Transcriptome-wide cross-linking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ~2,500 hnRNP A2/B1 binding sites and an unexpected role for hnRNP A2/B1 in alternative polyadenylation. Loss of hnRNP A2/B1 results in alternative splicing, including skipping of an exon in amyotrophic lateral sclerosis (ALS)-associated D-amino acid oxidase (DAO) that reduces D-serine metabolism. Inclusion of the DAO exon is also reduced in transgenic ALS mice models. ALS-associated hnRNP A2/B1 D290V mutant patient fibroblasts and motor neurons differentiated from induced pluripotent stem cells demonstrate gain-of-mutant-dependent splicing differences. Mutant motor neurons also exhibit increased hnRNP A2/B1 localization to cytoplasmic granules during stress, which are abrogated by a small molecule CA43.  Our findings and cellular resource identify RNA networks affected in loss of normal and mutated hnRNP A2/B1 with broad relevance to neurodegeneration.

overall_design: Microarray in mouse spinal after injection with ASO against hnRNP A2/B1 or saline. Three replicates per condition

first: Fernando

last: Martinez

first: Gabriel

middle: A

last: Pratt

first: Eric

last: Van Nostrand

first: Ranjan

last: Batra

first: Stephanie

last: Huelga

first: Katannya

last: Kapeli

first: Peter

last: Freese

first: Seung

first: Karen

last: Ling

first: Chelsea

last: Gelboin-Burkhart

first: Layla

last: Fijany

first: Harrison

first: Julia

last: Nussbacher

first: Hong-joo

last: Kim

first: Rea

last: Lardelli

first: Balaji

last: Sundararaman

first: John

last: Donohue

first: Jens

last: Lykke-Andersen

first: Frank

last: Bennett

first: Manuel

last: Ares Jr

first: Christopher

last: Burge

first: J

last: Taylor

last: Rigo


title: A custom genome-wide Plasmodium vivax 8x15K microarray for expression profiling of Indian clinical isolates showing complicated malaria

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

summary: High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n=14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n=85) present in the arrays showed perfect correlation (r2=0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r≥0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates.

overall_design: Plasmodium vivax isolates were collected from patients (n=14) with differing clinical symptoms. The patients exhibited symptoms categorized as uncomplicated (n=5) or complicated malaria (n=9). Criteria for determination of complicated malaria was based on World Health Organization, 2010 & 2015 guidelines. Parasite RNA material isolated from patients (n=14) was hybridized individually on this custom designed genome-wide P. vivax array on an Agilent 60mer 8x15K format. Microarray data analysis was performed to evaluate the performance of the array.

first: M

last: Raja

first: P

last: Boopathi

first: Amit

last: Subudhi

first: Dhanpat

last: Kochar

first: Sanjay