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_Stress]

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

country: USA

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 iPSC-MNs from patients with hnRNP A2/B1 D290V, VCP R155H, mutations or controls. Samples treated with puromycin or saline. 3 replicates per condition.

first: Fernando

middle: J

last: Martinez

first: Gabriel

middle: A

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

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

middle: B

last: Burge

first: J

last: Taylor

last: Rigo

middle: W


title: Differiential gene expression profiling in peripheral blood between pregnant sows versus non-pregnant sows

status: Public on Oct 16 2016

city: Beijing

first: Chuanli

last: Zhou

address: No.2 YuanmingyuanWest Road

department: Department of Animal Breeding and Genetics

country: China

institute: China Agricultural University

summary: To identify the molecular markers of early pregnancy in pigs, we compared global gene expression profiles of the maternal peripheral blood in pregnant sows with the non-pregnant sows. Peripheral blood sample was collected at 14 days after insemination from the submandibular vein of pregnant and non-pregnant sows respectively, and total RNA was isolated, purified and sent for microarray analysis. This study identified 127 up-regulated and 56 down-regulated genes (FC >= 1.5 and P < 0.05) in peripheral blood from pregnant sows versus non-pregnant sows. Of the differently expressed genes, nine (including LPAR3, RXFP4, GALP, CBR1, CBR2, GPX6, USP18, LHB and NR5A1) were found to exert function related to early pregnancy processes. Seven differentially expressed genes (CHGB, USP18, VWF, LPAR3, NR5A1, PPARD, BIN1) were selected to perform qRT-PCR in the same RNA samples.The expression profiles of these genes detected by qRT-PCR were consistent with those by microarray, which confirmed the reliability of our microarray data.

overall_design: To minimize the adverse effects of genetic heterogeneity in microarray experiments, three half-sib pairs and one unrelated pair were selected with four sows from the pregnancy group and the other four from the non-pregnancy group.

first: Ying

last: Yu

first: Junye

last: Shen


title: circulating miRNA in serum

status: Public on Oct 17 2016

city: Oslo

first: Ann Rita

last: Halvorsen

address: Montebello

country: Norway

institute: OUS- The Norwegian Radium Hospital

summary: Real-time qPCR analysis of miRNA in serum from lung cancer patients, COPD patients and healthy controls

overall_design: TotRNA was extractet from serum

first: Ann

middle: R

first: Åslaug

last: Helland


title: Copy number alterations in 8 lung cancer in Xuanwei samples

status: Public on Oct 22 2016

city: Kunming

first: Yanliang

last: Zhang

state: Yunnan province

address: No. 295, Xichang Road

department: Department of Clinical Laboratory

institute: First Affiliated Hospital of Kunming Medical University

type: Genome variation profiling by genome tiling array

summary: In order to screen potential novel 'driver genes' in lung cancer in Xuanwei (LCXW), genome-wide DNA copy number alterations (CNAs) were detected on 8 paired LCXW and non-cancerous lung (NCL) tissues by array-based comparative genomic hybridization microarrays. The log2 copy-number ratio calculation and CNA calls were determined using segMNT algorithm in NimbleScan. Log2 ratio test/control thresholds of 0.25 and -0.25 were defined as copy number gains and losses, respectively. Deviant signal intensity ratios involving 5 or more neighboring probes were considered as genomic aberrations. A large number of CNAs and DEGs were detected, respectively. Many recurrent CNAs were screened out, including gains at 5p15.33-p15.32, 5p15.1-p14.3 and 5p14.3-p14.2, and losses at 11q24.3, 21q21.1, 21q22.12-q22.13 and 21q22.2.

overall_design: 8 paired LCXW and NCL tissues were tested.

first: Yan

middle: L

first: Qiuyue

last: Xue

first: Guo

middle: Q

last: Pan

first: Xiao

middle: Y

last: Tuo

first: Xue

middle: M

last: Cai

first: Ya

last: Li

first: Tao

last: Huang

first: Xin

last: Duan

first: Yong


title: Expression data in mouse liver expressing or not the adapter Grb14

status: Public on Oct 28 2016

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary:
Grb14 is an endogenous inhibitor of insulin signaling
We used microarrays to investigate gene expression patterns after Grb14 silencing in mouse liver

overall_design: Ten week old mice were injected intraveinously with recombinant adenovirus expressing a control sh RNA (sh scramble) or a sh targetting Grb14 (shGrb14), and liver were studied in the fed state 2 days after the infection

first: Lucille

last: Morzyglod

first: Anne-Francoise

last: Burnol


title: Preferential Epigenetic Programming of Estrogen Response after in utero xenoestrogen (bisphenol-A) exposure [NimbleGen]

status: Public on Oct 24 2016

city: New Haven

first: Myles

middle: H

last: Alderman III

state: Ct

address: 10 Amistad St

department: Cell Biology

institute: Yale University School of Medicine

type: Methylation profiling by genome tiling array

summary: Bisphenol-A (BPA) is an environmentally ubiquitous estrogen-like endocrine-disrupting compound. Exposure  toBPAin utero hasbeen linked tofemale reproductive disorders, including endometrial hyperplasiaandbreast  cancer. Estrogens are an etiological factor in many of these conditions. We sought to determine whether in utero  exposure to BPA altered the globalCpGmethylation pattern of the uterine genome, subsequent gene expression, and  estrogen response.Pregnantmicewere exposed to an environmentally relevant dose of BPAorDMSOcontrol.Uterine  DNAand RNAwere examined by usingmethylatedDNAimmunoprecipitationmethylation microarray, expression  microarray, and quantitative PCR. In utero BPA exposure altered the global CpG methylation profile of the uterine  genome and subsequent gene expression. The effect on gene expression was not apparent until sexual maturation,  which suggested that estrogen response was the primary alteration. Indeed, prenatal BPA exposure preferentially  altered adult estrogen-responsive gene expression. Changes in estrogen response were accompanied by altered  methylation that preferentially affected estrogen receptor-a (ERa)–binding genes. The majority of genes that demonstrated  both altered expression and ERa binding had decreased methylation. BPA selectively altered the normal  developmental programming of estrogen-responsive genes via modification of the genes that bind ERa. Gene–  environment interactions driven by early life xenoestrogen exposure likely contributes to increased risk of estrogenrelateddisease  in adults.—Jorgensen, E. M.,Alderman,M.H., III,Taylor, H. S. Preferential epigenetic programmingof  estrogen response after in utero xenoestrogen (bisphenol-A) exposure.

overall_design: Dams were exposed to 5 mg/kg/day BPA or DMSO control for day 9-21 of pregnancy. Offspring were euthenized at 2 weeks and their uteri harvested. Samples are pooled by litter.

first: Elisa

last: Jorgensen

first: Hugh

middle: S

last: Taylor


title: Transcriptional profiling of the soil invertebrate (Folsomia candida) in pentachlorophenol contaminated soil

status: Public on Oct 30 2016

first: Min

last: Qiao

address: Shuangqing Road 18

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

summary: Pentachlorophenol (PCP) as a widely used pesticide is also considered to be an endocrine disruptor. Molecular effects of chemicals with endocrine disrupting potential on soil invertebrates are largely unknown. Collembola (Folsomia candida) has been used as a model organism in ecotoxicity and in this study we explored the transcriptional expression changes of Folsomia candida in response to PCP contamination. A total of 92 genes were significantly differentially expressed at all exposure time and majority of them were found to be down-regulated. In addition to the transcripts encoding cytochrome P450s and transferase enzymes, chitin-binding protein was also identified in the list of common differentially genes. Analyses of Gene Ontology (GO) annotation and enrichment revealed that cell cycle related transcripts were significantly induced by PCP, indicating it can stimulated the cell proliferation in springtail as reported in human breast cancer cells. We also observed enrichment of functional terms related to steroid receptor and particularly twenty significant differential expressed genes involved in Chitin metabolism in response to PCP exposure. Combined with the confirmation by qPCR, our results appears that the adverse effects on reproduction of springtails after exposure to PCP can be attributed to a chemical-induced delay in the molting cycle and molting associated genes may serve as possible biomarkers for toxicological effects. In general, analysis of changes in the gene expression profiles of springtails in response to PCP exposure is useful for obtaining information on endocrine disruptor exposure of soil invertebrate and may contribute to the classification and risk assessment of relative chemicals.

overall_design: Folsomia candida was exposed to pentachlorophenol spiked soil or untreated (reference/control) soil for 1, 2, and 7 days. For each time point 3 biological replicates were used, replicate samples consisted of total RNA extracted from 30 animals exposed in the same jar to either reference or pentachlorophenol spiked soil.

first: M

first: G

last: Wang

first: C

first: Y

middle: G

last: Zhu


title: Chlorpyrifos exposure zebrafish embryos

status: Public on Oct 14 2016

city: Amsterdam

first: Jessica

last: Legradi

address: De Boelelaan 1087

department: IVM

country: Netherlands

institute: VU Amsterdam

summary: Zebrafish embryos have been exposed to Chlorpyrifos from 24 to 48 hours post fertilization

overall_design: Two-condition experiment, control vs. Chlorpyrifos exposure embryos (7 mg/L), biological replicates: 3, dye swaps

first: L

last: Yang

first: J

last: Otte

first: U

last: Strahle


title: The genome-wide transcriptional response to light in Pseudomonas putida KT2440

status: Public on Oct 13 2016

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

type: Expression profiling by genome tiling array

summary: Pseudomonas putida KT2440 encodes 3 homologs of the LitR/CarH family (designated PplR1–PplR3; Pseudomonas putida light-induced transcription; regulator), which is an adenosyl B12-dependent light-sensitive MerR family transcriptional regulator. Transcriptome and individual transcriptional analysis revealed the existence of a number of photo-inducible genes including pplR1, phrB (encoding DNA photolyase), cfaA (cyclopropane synthase), folE (GTP cyclohydrolase I), cryB (cryptochrome-like protein), and multiple hypothetical genes. Transcriptional analysis based on a β-galactosidase reporter assay with single-, double-, and triple-knockout mutants of pplR1–pplR3 showed that deletion of pplR1–pplR3 completely abolished the light-inducible transcription in P. putida, which indicates that the transcription of light-inducible genes is under the ternary regulation of PplR proteins. DNase I footprint assay showed that PplR1 protein specifically binds to the promoter regions of light-inducible genes, suggesting a consensus PplR1-binding site, 5’-T(G/A)TACAn12TGTA(C/T)A-3’, predicted upon nucleotide sequence alignment. The disruption of cobalamin biosynthesis cluster did not affect the light-inducible transcription; however, disruption of ppSB1-LOV and ppSB2-LOV, a blue light photoreceptor genes, which are adjacent to pplR3 and pplR2, respectively, led to the complete loss of light-inducible transcription. Overall, the results suggest that 3 PplR and 2 PpSB-LOV regulate light-induced gene transcription in response to illumination. The high conservation of the pplR/ppSB-LOV cognate pair in Pseudomonas spp. suggests that the response and adaptation to light is similarly regulated in the group of non-phototrophic bacteria.

overall_design:
Chromosomal RNA maps of wild-type cells cultured under the light conditions were compared with those of wild-type cells cultured under the dark conditions
This is an Affymetrix custom-commercial tiling array that covers the Pseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density.  BPMAP files are provided as supplementary files. KT2440b520511FR-3.bpmap represents  the forward strand of KT2440 chromosome, and KT2440b520511FF-3.bpmap represents the reverse strand of KT2440 chromosome.

last: Takano

first: Naotaka

last: Mutaguchi

first: Teppei

last: Ebuchi

first: Hiroaki

last: Tsuchida

first: Takahiro

last: Yamamoto

first: Masaki

last: Shintani

first: Kenji

last: Ueda


title: Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light (3h time point)

status: Public on Oct 19 2016

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Photobiomodulation (PBM) with blue light induces a biphasic dose response curve in proliferation of immortalized human keratinocytes (HaCaT), with a maximum anti-proliferative effect reached with 30min (41.4J/cm²). The aim of this study was to test the photobiomodulatory effect of 41.4J/cm2 blue light irradiation on ROS production, apoptosis and gene expression at different time points after irradiation of HaCaT cells in vitro. ROS concentration was increased 30min after irradiation. However, already 1h after irradiation, cells were able to reduce ROS and balance the concentration to a normal level. The sudden increase in ROS did not damage the cells, which was demonstrated with FACS analysis where HaCaT cells did not show any sign of apoptosis after blue light irradiation. Furthermore, a time course could be seen in gene expression analysis after blue light, with an early response of stimulated genes already 1h after blue light irradiation, leading to the discovery of the aryl hydrocarbon receptor as possible target for blue light irradiation.

overall_design: 10,000 HaCaT cells per well were plated in black 96 well plates. After seeding, cells were incubated 24h at 37°C with 5% CO2. Medium was renewed and cells were irradiated for 30 min with blue light  (452nm). The right half of the plate was taped with black foil for the no light negative control. After defined time point (3h) cells were harvested

first: Anja

last: Becker

first: Norbert

last: Gretz


title: Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light (24h time point)

overall_design: 10,000 HaCaT cells per well were plated in black 96 well plates. After seeding, cells were incubated 24h at 37°C with 5% CO2. Medium was renewed and cells were irradiated for 30 min with blue light  (452nm). The right half of the plate was taped with black foil for the no light negative control. After defined time point (24h) cells were harvested


title: Expression data from newborn rat skeletal muscle subjected to low protein diet or low protein+taurine during gestation

city: Copenhagen N

first: Ole

middle: Hartvig

last: Mortensen

address: Panum 6.5.28, Blegdamsvej 3

department: Department of Biomedical Sciences

country: Denmark

institute: University of Copenhagen

summary:
Taurine ameliorates changes occurring in newborn skeletal muscle as a result of gestational protein restriction in C57BL/6 mice, but taurine supplementation effects may be exaggerated in C57BL/6 mice due to their inherent excessive taurinuria.  We examined if maternal taurine supplementation could ameliorate changes in gene expression levels, properties of mitochondria, myogenesis, and nutrient transport and sensing, in male newborn skeletal muscle caused by a maternal low protein (LP) diet in Wistar rats.  LP diet resulted in an 11% non-significant decrease in birth weight, which was not rescued by taurine supplementation (LP-Tau). LP-Tau offspring had signifi-cantly lower birth weight compared to controls. Gene expression profiling revealed 895 significantly changed genes, mainly an LP-induced down-regulation of genes involved in protein translation. Taurine fully or partially rescued 32% of these changes, but with no distinct pattern as to which genes were rescued.  Skeletal muscle taurine content in LP-Tau offspring was increased, but no changes in mRNA levels of the taurine synthesis pathway were observed. Taurine transporter mRNA levels, but not protein levels, were increased by LP diet.   Nutrient sensing pathways were largely unaffected in LP or LP-Tau groups, although taurine supplementation caused an unexpected decrease in total Akt and AMPK protein levels. PAT4 amino acid transporter mRNA was increased by LP, and normalized by taurine supplementation.  In conclusion, gestational protein restriction in rats decreased genes involved in protein translation in newborn skeletal muscle and led to changes in nutrient transporters. Taurine partly rescued these changes, hence underscoring the im-portance of taurine in development.
We used microarrays to detail changes in global programme of gene expression in newborn offspring skeletal muscle brains from rats subjected to either a control diet, a low protein diet or a low protein diet + taurine supplementation

overall_design: Pregnant Wistar rats were put on a control diet, a low protein diet or a low protein diet with taurine supplementation in the drinking water (2% w/v) starting day 1 of gestation. Newborn hind leg skeletal muscle from three male offspring of each dam was excised and pooled, followed by RNA extraction and hybridization on Affymetrix microarrays. Offspring from four dams from each group was used for the experiment resulting in a total number of samples of 12

first: Lea

last: Larsen

first: Sofie

last: Sandø-Pedersen

first: Laura

last: Ørstrup

first: Niels

last: Grunnet

first: Bjørn

last: Quistorff


title: Allyl-isothiocyanate treatment induces a complex transcriptional reprogramming including heat stress, oxidative stress and plant defense responses in Arabidopsis thaliana

status: Public on Oct 27 2016

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

institute: Norwegian University of Science and Technology

summary: Isothiocyanates (ITCs) are degradation products of the plant secondary metabolites glucosinolates (GSLs) and are known to affect human health as well as plant herbivores and pathogens. To investigate the processes engaged in plants upon exposure to isothiocyanate we performed a genome scale transcriptional profiling of Arabidopsis thaliana at different time points in response to an exogenous treatment with allyl-isothiocyanate.

overall_design: In-vitro grown Arabidopsis thaliana plants (10 days after sowing) were exposed to allyl-isothiocyanate vapour for 30 minutes, 1 hour and 9 hours. Non-exposed control plants were harvested at each time point. The plantlets used for each biological replica were harvested separately from two individual petri dishes and immediately flash-frozen in liquid N2. Each time point consists of two biological replicas from ITC-treated and control plants.

first: Ralph

last: Kissen

first: Ander

last: s Øverby

first: Atle

last: Bones

first: Torfinn

last: Sparstad


title: Copy number profiling of adenoid cystic carcinoma of the breast with high-grade transformation

status: Public on Oct 12 2016

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

summary: We sought to define the repertoire of somatic genetic alterations involved in the progression to high-grade TNBC (HG-TNBC) in two transformed AdCCs of the breast.

overall_design: Two patients with diagnosis of AdCC of the breast with heterogeneous morphology and associated with areas of HG-TNBC were included in the study. All diagnostic blocks and slides of both cases were centrally reviewed by four pathologists and morphologically distinct areas of each tumor were identified and microdissected. DNA for each case was hybridized on the molecular inverse probe assay using the OncoScan® FFPE Express custom service (Affymetrix, Santa Clara, CA).

first: Jorge

last: Reis-Filho

first: Britta

last: Weigelt


title: Copper toxicity response influences mesotrophic Synechococcus community structure

city: Livermore

first: Rhona

last: Stuart

address: 7000 East Ave.

institute: Lawrence Livermore National Laboratory

summary: Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, “species” also known as clades. We compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe-limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbor stress-tolerant subgroups, and thus fitness tradeoffs may govern Cu-tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.

sample_organism:
Bacteria
Synechococcus sp. CC9902

platform_organism:
Synechococcus sp. CC9311
Synechococcus sp. CC9902

overall_design: Two sets of experiments were performed. In the first, cultures of marine Synechococcus sp. strain CC9902 were grown to mid-exponential and treated with 0 (control) and 10 µM Cu (Cu-treated) for 2 h. Triplicates of each control and Cu-treated were run.  In the second experiment, Cu (8 nM) and control treatments were performed on triplicate field bottle incubations for 2 h, in the Southern California Bight.

first: Brian

last: Palenik


title: Differences in genome-wide gene expression response in PBMCs between young and old men upon caloric restriction

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Caloric restriction (CR) is considered to increase lifespan and to prevent various age-related diseases in different non-human organisms. Only a limited number of CR studies have been performed in humans, and results put CR as a beneficial tool to decrease risk factors in several age-related diseases. The question remains at what age CR should be implemented to be most effective with respect to healthy aging. The aim of our study was to elucidate the role of age in the transcriptional response to a 30% CR diet in immune cells, as immune response is affected during aging. Ten healthy young men, aged 20-34, and nine healthy old men, aged 64-85, were subjected to a two week weight maintenance diet, followed by three weeks of 30% CR. Before and after 30% CR, peripheral blood mononuclear cells’ (PBMCs) whole genome gene expression was assessed. Expression of 554 genes showed a different response between young and old men upon CR. Gene set enrichment analysis revealed a downregulation of gene sets involved in immune response in young men, but not in old men. At baseline, immune response-related genes were already higher expressed in old compared to young men. Upstream regulator analyses revealed that most potential regulators were controlling immune response, and were inhibited in young men upon CR, and activated in old men at baseline. Based on the gene expression data, we conclude that a short period of CR is more effective in young men compared to old men regarding immune related pathways.

overall_design: Gene expression was profiled in peripheral blood mononuclear cells (PBMCs) from young and old men before and after 30% caloric restriction.

first: I

last: van Bussel

first: J

last: Stoppelenburg

first: C

last: de Groot

first: M

last: Müller

first: L

last: Afman


title: Differentiated expression profiling between CD8+CD28+ T cell subset and CD8+CD28- T cell subset using long non coding RNA microarray in five healthy Chinese nonagenarians

status: Public on Oct 15 2016

city: Harbin

first: Yuhong

last: Wang

state: Heilongjiang

address: NO 23 Youzheng Street

institute: First Hospital of Harbin Medical University

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

summary:
To obtain the differentiated profiling of long noncoding RNA expression between CD8+CD28+ T cell subset and CD8+CD28- T cell subset, we have detecte lncRNA profiling between within-individual T cell subsets to identify differentiated lncRNA profiling in five apperant healthy Chinese nenogenarians who were cytomegalovirus-seropositive carriers. Human peripheral blood monocytes from these apperantly healthy CMV-seropositive nonagenarians was gathered. CD8+CD28+ T cells and CD8+CD28- T cells were further isolated using flow cytometry. Differentiated lncRNA profiling was compared between  CD8+CD28+ T cells and CD8+CD28- T cells using lncRNA microarry  detection within-individually. 586 lncRNAs were found significantly upregulated while 1113 lncRNAs were found significantly downregulated comparing CD8+CD28+ T cells with CD8+CD28- T cells in these Chinese nonagenarians with CMV seropositivity. Expression of ENST00000446590,NR_121652,NR_045006,ENST00000428936,NR_110375 from this differentiated profiling which were identified as previously domumented ageing-related lncRNAs were quantified in the same RNA samples by real-time PCR, confirming lncRNAs take critical role in regulating T cell immunosenesence in healthy nonagenarian Chinese CMV carriers.
Diffentiated lncRNA profiling was in-pair compared between total RNAs isolated from CD8+CD28+ T cells and CD8+CD28- T cells within-individually in Chinese nonagenarian CMV carriers.

overall_design: CD8+CD28+ T cell subset and CD8+CD28- T cell subset using long non coding RNA microarray in five healthy Chinese nenogenarians

first: Y

first: H

last: Han


title: piRNA expression data from mouse testis

city: Nanjing

first: Ling

last: Zhang

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

summary:
Pregnant females were distributed into two experimental groups: control group and MC-LR group which were exposed to 0 and 10 μg/L of MC-LR through drinking water separately during fetal and lactational periods. In 30 days old, the animals were euthanized.
Testes were determined to investigate the different expressions of piRNAs using a piRNA microarray.

overall_design: Pregnant mice were randomly divided into 2 groups: control group and MC-LR group, with each mouse kept separately. From gestation day 12 to postnatal day 21, 2 groups of pregnant mice were exposed to 0 and 10 μg/L of MC-LR through drinking water. The male offspring were breastfed after natural birth. 30 days after birth, the organs were promptly frozen in liquid nitrogen until further analysis.empty-2T, empty-4T, empty-5T were the three samples from 3 offsprings of different pregnant mice in control group. 10-3T, 10-4T, 10-7T were the three samples from 3 offsprings of different pregnant mice in MC-LR group.

first: Dongmei

last: Li


title: Molecular impact of electronic cigarette aerosol exposure in human bronchial epithelium

city: Boston

first: Elizabeth

last: Moses

state: Massachusetts

address: 72 E Concord St Rm E635

department: Computational Biomedicine

institute: Boston University

summary: Analysis of primary human bronchial epithelial cells grown in air liquid interface, exposed in vitro to whole tobacco cigarette smoke (48 puffs, 48 minutes) and electronic cigarette aerosol (400 puffs, 200 minutes). Electronic cigarette exposures included two flavors (menthol, tobacco) both with, and without nicotine.

overall_design: Human bronchial epithelial cells were exposed to whole tobacco cigarette smoke (n=3), Blu e-cig tobacco flavor, no nicotine (n=3), Blu e-cig tobacco flavor, with nicotine (n=3), Blu e-cig menthol flavor, no nicotine (n=3), Blu e-cig menthol flavor, with nicotine (n=3) or air controls (n=3) in a Vitrocell smoking machine and then rested for 24 hours.

first: Teresa

first: Sean

last: Corbett

first: Marc

last: Lenburg

first: Avi

last: Spira


title: Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light (1h time point)

first: Carsten

last: Sticht

overall_design: 10,000 HaCaT cells per well were plated in black 96 well plates. After seeding, cells were incubated 24h at 37°C with 5% CO2. Medium was renewed and cells were irradiated for 30 min with blue light  (452nm). The right half of the plate was taped with black foil for the no light negative control. After defined time point (1h) cells were harvested

first: Anja

last: Becker

first: Norbert

last: Gretz


title: Developing gene signature against Mycobacterium bovis infection in Cattle

status: Public on Oct 25 2016

city: Bareillly

first: SANJEEV

middle: KUMAR

last: SHUKLA

state: UTTAR PRADESH

address: IZATNAGAR

department: Division of Animal Genetics

country: India

institute: Indian Veterinary Research Institute

summary: The bTB research programme is centred on identifying the genetic basis for resistance against bovine tuberculosis and towards diagnostics

sample_organism:
Bos primigenius
Bos taurus
Bos indicus
Bubalus bubalis

overall_design: Agilent Whole Genome Bovine 8x60k Gene Expression  (AMADID: 29411)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Sanjeev

last: Shukla

first: Shubhra

first: Anuj

last: Chuhan

first: Sandeep

last: Maurya

first: Deepak

last: Sharma


title: Renal gene expression changes in p53 heterozygous and p53 homozygous mice due to chronic dietary exposure to the mycotoxin ochratoxin A

city: Ottawa

first: Ivan

last: Curran

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Protection Food Branch

country: Canada

institute: Health Canada

summary: Changes in renal gene expression were assessed in p53WT(+/+) mice and their heterozygous p53TG(+/-) counterparts exposed to the nephrotoxic and tumourigenic fungal toxin Ochratoxin A (OTA) in their diet for 26 weeks.  The p53TG mouse model has been used in screening for potential carcinogens as it displays increased sensitivity to genotoxic carcinogens.  Comparison between the effects of OTA in diet on male mice of these two strains was assessed at 0, 0.05, 2.0, 10.0 mg OTA/kg diet.  Changes in global gene expression were compared using Agilent Mouse oligonucleotide microarray analysis of kidneys from control (0 mg OTA/kg diet) and treated (2 mg OTA/kg diet) mice.  Significant changes in gene expression associated with cell cycle regulation, DNA damage repair, tumour suppression and apoptosis were consistent with nephrotoxicity due to OTA exposure in both mouse strains. Changes in genes related to oxidative stress and free radical scavenging may contribute to the down-regulation by OTA of genes associated with metabolism. Gene expression changes were consistent with phenotype and provided insight on the cellular responses to chronic OTA exposure.

overall_design: Kidneys from male p53WT mice and their heterozygous p53TG counterparts were collected at terminal necropsy from control mice and mice exposed to 2 mg OTA/kg diet for 26 weeks.

first: A

last: Nunnikhoven

first: I

first: D

middle: E

last: Pinke

last: Gannon

first: L

last: Coady

first: C

last: Qiao

first: V

last: Liston

last: Lefebvre

first: R

last: Mehta

first: G

last: Bondy


title: Aroclor exposure zebrafish embryos

first: Jessica

last: Legradi

summary: Zebrafish embryos have been exposed to Aroclor 1254 from 24 to 48 hours post fertilization

overall_design: Two-condition experiment, control vs Aroclor exposure embryos (71.9 mg/L), biological replicates: 3, dye swaps

last: Yang

first: J

middle: C

last: Otte

first: U

last: Strahle


title: Analysis of Fusarium verticillioides gene expression in response to 2-benzoxazolinone (BOA)

city: Athens

first: Anthony

middle: E.

last: Glenn

state: GA

address: 950 College Station Rd

department: Toxicology & Mycotoxin Research Unit

institute: USDA, ARS, USNPRC, R.B. Russell Research Center

summary: Investigation of whole genome gene expression level changes in F. verticillioides FRC M-3125 when exposed to 50 ug/ml 2-benzoxazolinone (BOA).  Cultures were harvested two hours after exposure.  Assessed in reference to control cultures of M-3125 exposed to ethanol (1% final concentration) since BOA was dissolved in ethanol.

overall_design: A four chip study using total RNA recovered from two separate control cultures of F. verticillioides FRC M-3125 in PDB containing 1% ethanol and two separate experimental cultures of M-3125 grown in PDB plus the added treatment of 50 ug/ml ethanolic BOA.  The cultures were incubated for two hours on a rotary shaker (200 rpm) at 27C in the dark and then harvested by vacuum filtration and frozen in liquid nitrogen. The chips were a F. verticillioides custom 14K array based on platform GPL14669.


title: Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light

first: Carsten

last: Sticht

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

overall_design: Refer to individual Series


title: Characterisation of Burkholderia pseudomallei colony morphology variants by microarray

city: Kuala Lumpur

first: Anis

middle: Rageh

last: Al-Maleki

address: Faculty of medicine, University of Malaya

department: Departement of medical microbiology

country: Malaysia

institute: University of Malaya

summary: Burkholderia pseudomallei  is the causative agent of melioidosis which is endemic to Southeast Asia and Northern Australia. It is a Gram-negative soil and water bacterium that represents a potential bioterrorism threat. Colony morphology variation is a remarkable feature in primary clinical cultures of B. pseudomallei. Differences in expression of several potential virulence and survival genes were believed to be associated with B. pseudomallei colony morphology variants. Microarrray approach was used to investigate alterations of the global B. pseudomallei transcriptome profile at the mid-logarithmic phase of growth, among the wild type (WT) and small colony variant (SCV) of B. pseudomallei pre- and post-exposed to human lung epithelial cells, A549. Generally, SCV pre- and post-exposed have lower metabolic requirements and consume lesser energy than WT pre- and post-exposed to A549; however, both WT and SCV may limit their metabolic activity during the infection of A549 cells and this is indicated by the down-regulation of genes implicated in metabolism of amino acids, carbohydrate, lipid, and  other amino acids, and biodegradation of xenobiotics. On the other hand, many well-known virulence and survival factors including T3SS, T6SS, fimbriae, capsular polysaccharides, drug resistance and stress response were up-regulated in both WT and SCV pre- and post-exposed to A549 cells.  Several virulence factors expressed at the mid-logarithmic phase of growth. Microarray analysis on the different morphotypes demonstrated the essential difference in bacterial response associated with virulence and survival pre- and post-exposed to A549 cells.

overall_design:
The Agilent-019078 Custom B. pseudomallei 8X15K microarray chip (Agilent,  GEO reference GPL13233), designed by Chieng S et al., (2012) (Chieng et al., 2012) was used as the platform to inspect the changes in the gene expression of B. pseudomallei WT and SCV morphotypes pre- and post-exposed to A549 human lung epithelial cells, (Figure 2.7). Four biological replicates were used for each set of the experiments. The chip was designed for the analysis of 5,721 non-cross-hybridising ORFs of B. pseudomallei K96243. The 5,721 probe sequences were randomly replicated and distributed in a microarray of 15,000 probes to fit Agilent 8 × 15 K microarray format. Figure 2.7 shows the microarray experimental design scheme of the gene expression studies.
The quality control data obtained confirmed that all the arrays on the microarray chip met the expected quality control, however one replicate among the 4 replicates have been excluded for the following samples (SCV pre-exposed, WT post-exposed and SCV post-exposed).


title: Microarray analysis of gene expression in liver, adipose tissue and skeletal muscle in response to chronic dietary administration of NDGA to high-fructose fed dyslipidemic rats

city: Palo Alto

first: Wen-Jun

last: Shen

address: 3801 Miranda Avenue

department: Medicine

institute: Stanford University

summary: A high-fructose diet (HFrD) fed rat model of hypertriglyceridemia, dyslipidemia, insulin resistance and hepatic steatosis was employed to investigate the global transcriptional changes in the lipid metabolizing pathways in three insulin sensitive tissues:, liver, skeletal muscle and adipose tissue in response to chronic dietary administration of NDGA.

overall_design: Sprague-Dawley male rats (SD) were fed a chow (control) diet, high-fructose diet (HFrD) or HFrD supplemented with NDGA (2.4 g/kg diet) for eight weeks. Dietary administration of NDGA decreased plasma levels of TG, glucose, and insulin, and attenuated hepatic TG accumulation. DNA microarray expression profiling was performed on RNA isolated from liver, adipose and muscle.

first: Haiyan

last: Zhang

first: Yihang

last: Li

first: Alex

last: Bittner

first: Stefanie

first: Juveria

last: Tabassum

first: Yuan

middle: F

last: Cortez

first: Fredric

middle: B

last: Kreamer

first: Salman

last: Azhar


title: Gender differences in the cytokines and chemokines gene expression profiles within the medulla oblongata of SHRs

first: Sabine

last: Gouraud

address: 3-10-2  Osawa, Mitaka

institute: International Christian University

summary:
Medulla oblongata is a region of the brain containing multiple blood pressure regulation centers, including the nucleus of the solitary tract (NTS), a pivotal region for regulating the set-point of arterial pressure. Our previous findings suggest that the NTS of male pre-hypertensive rats and spontaneously hypertensive rats (SHRs) exhibits abnormal inflammatory condition compared with that of normotensive Wistar-Kyoto (WKY) rats. Females of SHRs exhibit a lower blood pressure than their male counterpart but the molecular mechanism is not well described.
To unveil the gender differences in the central regulation of blood pressure, we investigated the gene expression profile of cytokines and chemokines in the medulla oblongata of female SHRs compared to that of their male counterparts.

overall_design: The medulla oblongata from six adult SHRs (males=3, females=3) were dissected. Total RNAs were extracted from each tissue sample by using Trizol method. Equal amounts of total RNAs were submitted separately to qPCR gene expression profiling experiments by using the Rat Cytokines & Chemokines qPCR array and by following the manufacturer's recommendation.

first: Makiko

last: Onishi

first: Kei

last: Hashimoto

first: Yasunori

last: Miyamoto

first: Hidefumi

last: Waki


title: Microarray expression profile from YAP1 knockdown in DDX3-overexpressing colorectal cancer cells

status: Public on Oct 18 2016

city: Taipei

first: Huei

last: Lee

address: Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Room 5, 12F, F building, No. 3, Park Street, Nangang District

country: Taiwan

institute: Taipei Medical University/ Graduate Institute of Cancer Biology and Drug Discovery

summary: To identify which genes could be modulated by the DDX3-YAP1 axis in SW48 cells.

overall_design: YAP1-knockdown in DDX3-overexpressing SW48 cells were analyzed compare to control and DDX3-overexpressing SW48 cells

first: De-Wei

last: Wu


title: Transcriptomic differences between E. coli BL21 and K-12 MG1655 during n-heptanoic acid stress

status: Public on Oct 11 2016

city: Seoul

first: Ji-Min

last: Woo

address: Ewhayeodae-gil

country: South Korea

institute: Ewha womans university

summary: Biosynthesis of carboxylic acids and fatty acids from renewable biomass is a key issue in biorefinery. However, their productivities are often limited due to various toxic effects of the products on the host organisms. Here, we have investigated the factors that influence tolerance of Escherichia coli to long chain carboxylic acid (e.g., n-heptanoic acid)-induced stress by using transcriptome analysis. The metabolic and genomic responses of E. coli BL21 and MG1655 strains with n-heptanoic acid indicated that acid stress is one of the major stresses, which might be generated by n-heptanoic acid in addition to the presumed solvent-like stress.

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

overall_design: E. coli cells were grown to the exponential growth phase (OD600 = 0.5), 3 or 10 mM heptanoic acid was treated to BL21(DE3) and K-12 MG1655, respectively. After 3 h incubation, the E. coli cells were harvested for Microarray analysis.

first: Jin-Byung

last: Park


title: OBP4 modifies root growth, cell elongation and callus formation

status: Public on Oct 06 2016

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

summary:
Investigation of whole genome gene expression level changes in Arabidopsis roots by overexpressing OBP4 transcription factor under teh control of an estradiol inducible promoter
This work analyzes the effect of overexpression the transcription factor OBP4 in gene transcription. Details of how ectopic expression affects root development and callus formation are described in Rammirez-Parra et al. (submitted)

overall_design: A six chip study using total RNA extracted from three independent experiments of Arabidopsis roots overexpressiong GFP and three  independent experiments of Arabidopsis roots overexpressing OBP4 during 8 hours.

first: Elene

last: Ramirez-Parra


title: Genomic profiling of stage II and III colon cancers reveals APC mutations to be associated with survival in stage III colon cancer patients

status: Public on Oct 10 2016

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: This study aims to stratify stage II and III colon cancer patients for risk of disease recurrence based on DNA aberrations, including DNA copy number aberrations (CNA) and CNA-associated chromosomal breakpoints. To this end, high quality array-CGH data of clinically well-annotated colon cancer specimens was generated using FFPE material from a selected series of primary tumor and patient-matched normal tissue.

overall_design: arrayCGH data of 114 stage II and III colon cancers.

first: Evert

last: van den Broek

first: Oscar

last: Krijgsman

first: Marianne

last: Tijssen

first: Hendrik

last: van Essen

first: Sandra

last: Mongera

first: Mark

middle: A

last: van de Wiel

first: Eric

middle: J

last: Belt

first: Sjoerd

last: den Uil

first: Herman

last: Bril

first: Hein

last: Stockmann

first: Beatriz

last: Carvalho

first: Bauke

last: Ylstra

first: Gerrit

last: Meijer

first: Remond

last: Fijneman


title: Evidence for conflict at the molecular level, and a possible solution to it - gene regulation

city: Cleveland

first: Yibayiri

middle: Osee

last: Sanogo

state: OH

address: 9500 S Euclid Ave

department: Genomics Core

institute: Cleveland Clinic Foundation

summary: We investigated the transcriptomic response to courtship opportunity in four regions of the brain (telencephalon, diencephalon, cerebellum and brain stem) of a teleost fish, the threespined stickleback (Gasterosteus aculeatus). We tested the hypothesis that gene regulatory networks modulate the transcriptional response tocourtship opportunity in the different brain regions and thereby mating. Indeed, transcription regulatory network analysis identified cis-regulatory transcription factor motifs enriched in upregulated genes in one brain region and downregulated in the others. We further validated our findings by qPCR.

overall_design: 2 conditions: control fish and fish that were presented a female on their territory,  Biological replicates 6. Four brain regions.

middle: O

last: Band

first: Alison

last: Bell


title: Pathophysiological role of hepatocyte nuclear factor 6 (HNF6) during cholestatic liver injury

city: Peoria

first: Kewei

last: Wang

state: IL

address: One Illini Dr.

institute: Univ. of Illinois College of Medicine at Peoria

type: Genome binding/occupancy profiling by genome tiling array

summary: Animal models of parenchymal liver injury by bile duct ligation (BDL) and all forms of liver diseases including neonatal hepatitis and clinical obstructive cholangiopathies such as biliary atresia have the pathological features of cholestasis and liver dysfunction. Hepatocyte nuclear factors 6 (HNF6) is important to the transcriptional regulation, expression and function of essential hepatic genes involved in the differentiated as well as the adaptive response to liver injury. Using HNF6 conditional knock out mice where HNF6 is functionally deleted in the liver, we established that HNF6 is required for proper liver function of cholesterol clearance, improvement of cholestasis and hepatocyte regeneration. Enhancing HNF6 expression in wild type mice also diminished hepatic apoptosis and fibrosis. In this proposal, we propose to further characterize the biological function of HNF6 by testing the HYPOTHESIS that HNF6 direct transcriptional regulation of antiapoptotic and antifibrotic pathways contributes to hepatoprotection during bile duct injury. This hypothesis will be tested in two specific aims.

overall_design: Livers were isolated from wild-type (WT) and HNF6 knockout (KO) mice respectively. Liver samples were processed via ChIP protocol using monoclonal HNF6 or IgG antibodies (control). ChIP-DNA was further processed by Affymetrix Procedure H. The following samples are PCR products: (1) wild-type liver 1 & HNF6 antibody; (2) wild-type liver 2 & HNF6 antibody; (3) wild-type liver 1 & IgG antibody; (4) wild-type liver 2 & IgG antibody; (5) HNF6-knockout liver 1 & HNF6 antibody; (6) HNF6-knockout liver 1 & HNF6 antibody.

first: Minhua

first: Maureen

last: Gannon

first: Ai-Xuan

last: Holterman


title: Molecular analysis of renal cell carcinoma with unclassfied histology [copy number alterations]

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Renal cell carcinomas with unclassified histology (uRCC) constitute a significant portion of aggressive non-clear cell RCC (nccRCC) that have no standard therapy. The oncogenic drivers in these tumors are unknown. We performed a molecular analysis of 62 high-grade primary uRCC, incorporating targeted cancer gene sequencing, RNA sequencing, Single Nucleotide Polymorphism array, fluorescence in-situ hybridization, immunohistochemistry, and cell-based assays. We identified recurrent somatic mutations in 29 genes, including NF2 (18%), SETD2 (18%), BAP1 (13%), KMT2C (10%), and MTOR (8%). Integrated analysis revealed distinct molecular subsets, including a subset of 26% uRCC characterized by NF2-loss, dysregulated Hippo-YAP pathway and worse survival.

overall_design: Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from paraffin embedded formalin fixed tumor tissues from 15 unclassified renal cell carcinomas.  Genome-wide DNA copy number alterations and allelic imbalances were analyzed.

first: Ying-Bei

last: Chen

first: Lu


title: Molecular signatures of infection-induced immunity against Bordetella pertussis.

status: Public on Oct 08 2016

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

summary:
Murine lung gene expression responses to primary and secondary infection with Bordetella pertussis.
Data were compared to other parameters such as flow cytometry and multiplex immunoassays.

overall_design: A 33 array study based on a common reference design.

first: Rene

last: Raeven


title: Molecular classification of non-keratinizing nasopharyngeal carcinoma using mRNA expression profiling

status: Public on Oct 05 2016

city: Guangzhou

first: Zhong-Xi

last: Huang

address: Tonghe

department: Cancer Institute

institute: Southern Medical University

summary: To uncover potential molecular subtypes of non-keratinizing nasopharyngeal carcinoma, gene expression profiles of primary NK-NPCs and NPs were conducted and analyzed using bioinformatics methods.

overall_design: We collected 25 primary NK-NPCs and 8 nasopharynx tissues obtained from patients with inflamed nasopharyngeal mucosa. mRNA expression profiling was performed followed by bioinformatics analysis.

first: K

middle: T

last: Yao

first: Z

middle: X


title: Transcriptome analysis of Pseudomonas aeruginosa PAO1 WT, ΔpauA2 mutant, and ΔpauA2 suppressor

status: Public on Oct 01 2016

city: Atlanta

first: Yu Chih

last: Peng

state: Georgia

address: 100 Piedmont Ave SE

department: Biology

institute: Georgia State University

summary: PauA2 plays an essential role in spermine catabolism and that exogenous spermine exerts a bactericidal effect on the ΔpauA2 mutant of P. aeruginosa. Not only subjected to growth inhibition by spermine, the pauA2 mutant without a functional γ-glutamylpolyamine synthetase PauA2 became more sensitive to β-lactam antibiotics in human serum. To explore PauA2 as a potential target of drug development, suppressors of the pauA2 mutant were isolated from selection plates containing spermine. These suppressors share common changes in various phenotypes. Genome resequencing of a representative suppressor revealed a unique mutation at the phoU gene, and a constitutive expression of the Pho regulon as evidenced by measurements of transcriptome analysis.

overall_design: We conducted two independent microarray experiments for each of strains. P. aeruginosa PAO1 and its derivatives was grown aerobically in LB broth along with 300 rpm shaking at 37°C.

first: Yu-Chih

first: Chung-Dar

last: Lu


title: Does broodstock nutritional history affect the response of progeny to different first-feeding diets? A whole-body transcriptomic study of rainbow trout alevins

status: Public on Oct 03 2016

city: Saint-Pée sur Nivelle

first: Viviana

last: Lazzarotto

address: Quartier Ibarron

institute: INRA

summary: The whole-body transcriptome of trout alevins was characterized to investigate the effects of long-term feeding of rainbow trout broodstock females a diet free of fishmeal (FM) and fish oil (FO) on the metabolic capacities of progeny. Effects were studied before first feeding and after 3 weeks of feeding with diets containing different proportions of marine and plant ingredients. We showed that that maternal diet history did not significantly affect expression of any gene before the first feeding. We found an effect of maternal nutritional history on gene expression in alevins after 3 weeks of feeding. The major differences in the transcriptome of alevins from VEG-fed females compared to those from COM-fed females were: (i) a down-regulation of genes involved in muscle growth/contraction and (ii) a higher level of expression of genes involved in carbohydrate and energy metabolism related to the delay in growth/ development observed with plant-based diets. Our findings also showed an effect of the first-feeding diets, irrespective of maternal nutritional history. Specifically, the introduction of plant ingredients resulted in up-regulation of genes involved in AA/protein and cholesterol metabolism and in differences in the expression of genes related to carbohydrate metabolism.

overall_design:
Transcriptomic response were studied in whole-body alevins from two broodstock groups collected before the first feeding (n=8/broodstock group) and after three weeks of feeding one of the three experimental diets (n=8/diet/broodstock group);

COM = Broodstock commercial diet
VEG = Broodstock totally plant-based diet (free of FM and FO)
COM_M = Alevins from broodstock fed the COM diet, receiving a (FM-FO based) Marine diet for 3 wks
COM_C = Alevins from broodstock fed the COM diet, receiving a commercial-like diet (mixed: plant-based and marine (FM&FO) ingredients) for 3 wks
COM_V = Alevins from broodstock fed the COM diet, receiving a totally plant-based diet for 3 wks
VEG_M = Alevins from broodstock fed the VEG diet, receiving a (FM-FO based) Marine diet for 3 wks
VEG_C = Alevins from broodstock fed the VEG diet, receiving a commercial-like diet (mixed: plant-based and marine (FM&FO) ingredients) for 3 wks
VEG_V = Alevins from broodstock fed the VEG diet, receiving a totally plant-based diet for 3 wks

first: Geneviève

last: Corraze

first: Laurence

last: Larroquet

first: David

last: Mazurais

first: Françoise

last: Médale


title: The Challenge of Stability in High-Throughput Gene Expression Analysis: Comprehensive Selection and Evaluation of Reference Genes for BALB/c Mice Spleen Samples in the Leishmania infantum Infection Model.

city: La Laguna

first: Emma

last: Carmelo

state: SANTA CRUZ DE TENERIFE

address: C/ Astrofisico Francisco Sanchez s/n, Campus de Anchieta

department: University Institute of Tropical Diseases and Public Health

institute: University of La Laguna

summary: The interaction of Leishmania with BALB/c mice induces dramatic changes in transcriptome patterns in the parasite, but also in the target organs (spleen, liver…) due to its response against infection. Real-time quantitative PCR (qPCR) is an interesting approach to analyze these changes and understand the immunological pathways that lead to protection or progression of disease. However, qPCR results need to be normalized against one or more reference genes (RG) to correct for non-specific experimental variation. The development of technical platforms for high-throughput qPCR analysis, and powerful software for analysis of qPCR data, have acknowledged the problem that some reference genes widely used due to their known or suspected "housekeeping" roles, should be avoided due to high expression variability across different tissues or experimental conditions. In this paper we evaluated the stability of 112 genes using three different algorithms: geNorm, NormFinder and RefFinder in spleen samples from BALB/c mice under different experimental conditions (control and Leishmania infantum-infected mice). Despite minor discrepancies in the stability ranking shown by the three methods, most genes show very similar performance as RG (either good or poor) across this massive data set. Our results show that some of the genes traditionally used as RG in this model (i.e. B2m, Polr2a and Tbp) are clearly outperformed by others. In particular, the combination of Il2rg + Itgb2 was identified among the best scoring candidate RG for every group of mice and every algorithm used in this experimental model. Finally, we have demonstrated that using "traditional" vs rationally-selected RG for normalization of gene expression data may lead to loss of statistical significance of gene expression changes when using large-scale platforms, and therefore misinterpretation of results. Taken together, our results highlight the need for a comprehensive, high-throughput search for the most stable reference genes in each particular experimental model

overall_design:
47 BALB/c  mice (14-15 weeks old) were used  in this study. Mice were randomly separated in two groups: (i) 23 control mice and (ii) 24 mice  that were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein. Mice were euthanized by cervical dislocation and spleens were removed and immediately stored in RNAlater at -70C. After RNA extraction and reverse transcription, Real-time PCR was performed using QuantStudio 12K Flex Real-Time PCR System  following manufacturer’s instructions, using Custom TaqMan OpenArray Real-Time PCR Plates. Ct values obtained from RT-qPCR were analized  by  three different algorithms (geNorm,  NormFinder and RefFinder) in order to evaluate the stability of the 112 genes and identify the most suitable for normalization of gene expression.

Please note that the three algorithms were used for the identification of the best Reference genes in all samples. Once identified, those RG were used to normalize gene expression using geNorm only.

The sample data table includes the normalized data using Il2rg+Itgb2 as reference genes, as identified and validated in the associated publication.

The 'geNorm_Polr2a_Tbp_normalized.txt' includes the data normalized using Polr2a+Tbp as reference genes, two reference genes traditionally used in the literature for this model.

first: Yasmina

last: Hernandez-Santana

first: Eduardo

last: Ontoria

first: Ana

last: Gonzalez-García

first: Antonieta

last: Quispe-Ricalde

first: Vicente

last: Larraga

first: Basilio

last: Valladares


title: Prefrontal cortex gene expression signature in autistic BTBR mice

city: Dublin

last: Henshall

address: 123 St Stephens Green

country: Ireland

institute: Royal College of Surgeons in Ireland

summary: Autism spectrum disorders (ASD) are characterized by a high degree of genetic heterogeneity. Genomic studies identified common pathological processes underlying the heterogeneous clinical manifestations of ASD, and transcriptome analyses revealed that gene networks involved in synapse development, neuronal activity and immune function are deregulated in ASD. Mouse models provide unique tools to investigate the neurobiological basis of ASD. Here we used the BTBR (BTBR T+ Itpr3tf/J) ASD mouse model to identify conserved ASD-related molecular signatures.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: microRNA expression in the BTBR mouse prefrontal cortex was measured by TaqMan OpenArray Rodent MicroRNA Panel and compared to the microRNA expression profile of C57Bl6/J controls (5 months old, n= 3 mice per group).

first: Catherine

last: Mooney

first: Yuri

last: Bozzi

first: Giovanni

last: Provenzano

first: Eva

last: Jimenez

first: Laura

last: Ricceri

first: Maria-Luisa

last: Scattoni


title: Gene expression data from longissimus dorsi muscle 25-day-old male pigs

city: Changsha

first: Haiming

last: Ma

state: Hunan

address: Nongda road NO.1

institute: Hunan Agricultural University

summary:
To explore the difference in gene expression in the Yorshire and Shaziling pig, and could contribute to further studies on porcine myogenesis and adipogenesis, we studied the mRNA expression profile using microarray technique.
We used microarrays to detail the global programme of gene expression and identified the difference between the two pig breeds during this process.

overall_design: These pigs were selected at the early stage for RNA extraction and hybridization on Affymetrix microarrays,were Yorshire and Shaziling pig, each breed has three replicates.

first: Dong

last: Xu

first: Jun

last: He


title: Mosaic Klinefelter Syndrome testicular gene expression profile by a whole genome microarray approach.

city: Chieti

first: Valentina

last: Gatta

state: Abruzzo

address: Via Colle Dell'Ara

department: Department of Psychological SciencesDepartment of Psychological Sciences

institute: University G.d'Annunzio

summary:
Objective: Klinefelter Syndrome (KS) is the most common sexual chromosome abnormality (47,XXY; 46,XY/47XXY) and represents the first genetic cause of male infertility. The mechanisms leading to KS testis degeneration are still unclear and no therapy is so far available for affected patients.
The present study is aimed to unravel information about molecules playing a key role in the disruption of the spermatogenesis in mosaic oligospermic KS patients.
Design: Gene expression profiles analysis of KS mosaic oligospermic testis versus normal testis, could provide useful information about the molecular basis of the alteration of the spermatogenesis.
Materials and Methods: Transcriptome analysis was performed carrying out gene expression profile by a whole genome microarray approach on testis biopsies obtained from 3 oligopermic mosaic KS men and from 3 controls, for a total of 6 experiments. T-test and False Discovery Rate were used to evaluate differentially expressed genes. Identified transcripts were analysed by Ingenuity Pathways Analysis software to disclose genes biological functions.
Results: Data analysis revealed the differentially up- and down-expression, in mosaic KS testis versus the control ones, of respectively 303 and 747  genes related to Endocrine system disorders, Lipid metabolism, Reproductive disease, cell and organ morphology, and cell death.
Conclusions: Taken together these data show the presence of several de-regulated genes involved in mosaic KS testis failure. Data show the defects in sperm production and development and defects within the somatic component of the testis.
This information, associated with an early diagnosis could help to unravel possible therapeutic targets for testis failure prevention and limitation.

overall_design: Gene expression profile of 3 oligozoospermic mosaic KS testicular biopsies versus 3 pooled control testicular biposies form patients with normal spermatogenesis. A total of 6 experiments was carried out including biological and technical replicates.


title: Integrative Analysis of miRNA and mRNA Paired Expression Profiling of Primary Fibroblast Derived from Diabetic Foot Ulcers Reveals Multiple Impaired Cellular Functions

city: MIAMI

first: Marjana

last: Tomic-Canic

address: 1600 SW 10th Ave, RMSB RM2029A

institute: University of Miami

summary: Diabetic foot ulcers (DFUs) are one of the major complications of diabetes. Its molecular pathology remains poorly understood, impeding the development of effective treatments. Although it has been established that multiple cell types, including fibroblasts, keratinocytes, macrophages and endothelial cells, all contribute to inhibition of healing, less is known regarding individual contributions of each cell type. Thus, we generated primary fibroblasts from non-healing DFUs and evaluated their cellular and molecular properties in comparison to non-diabetic foot fibroblasts (NFFs). Specifically, we analyzed both micro-RNA and mRNA expression profiles of primary DFU fibroblasts. These paired genomic analyses identified a total of 331 reciprocal miRNA-mRNA pairs (21 miRNAs (FC>2.0) along with 239 predicted target genes (FC>1.5) that are significantly and differentially expressed. Of these, we focused on three miRNAs (miR-21-5p, miR-34a-5p, miR-145-5p) found to be induced in DFU fibroblasts as most differentially regulated. Their involvement in cellular functions important for wound healing was investigated by testing the expression of their downstream targets as well as by quantifying cellular behaviors in a prospectively collected and generated cell lines from 15 patients (7 DFUF and 8 NFF samples). We found large number of downstream targets of miR-21-5p, miR-34a-5p, miR-145-5p to be coordinately regulated in mRNA profiles, which was confirmed by qPCR. Genomic analysis of miR-21-5p, miR-34a-5p, miR-145-5p and their target genes indicates that these are contributing to the inhibition of cell movement and cell proliferation, together with increased cell differentiation and senescence in DFU fibroblasts, which was confirmed by cellular assays. We conclude that induction of miR-21-5p, miR-34a-5p, miR-145-5p in DFU dermal fibroblasts plays an important role in impairing multiple cellular functions, thus contributing to overall inhibition of healing in DFUs.

overall_design:
foot skin biopsies obtained from diabetic and non-diabetic people were thoroughly washed in DMEM supplemented with 2× Penicillin/Streptomycin/Fungizone, and gentamicin (50mg/L). After, the epidermis was removed from specimens, the dermis was finely minced and placed in 12-well plates. For the establishment of fibroblast cultures, DMEM (Life Technologies) supplemented with 10% FBS, HEPES (1.9mg/ml), streptomycin (100 μg/ml), penicillin (100 U/ml), and Fungizone Antimycotic (0.25 µg/mL) was used. RNA was isolated from cells (passage 1 or 2) using miRNeasy Mini Kit (QIAGEN).    miR expression profiles of DFUF and NFF fibroblasts were generated by nanoString nCounter miR Expression Assays (NanoString Technologies, Seattle, WA, USA) and analyzed using nSolver2.0 software following manufacturer's instructions. Data were normalized to gene controls included in the assays.
-----------------------
This represents the miRNA component only

first: Liang

last: Liang

first: Rivka

last: Stone

first: Olivera

last: Stojadinovic

first: Horacio

last: Ramirez

first: Anna

middle: G

last: Maione

first: Avi

last: Smith

first: Vanessa

last: Yanez

first: Aristides

last: Veves

first: Robert

middle: S

last: Kirsner

first: Jonathan

last: Garlick


title: Genomic profiling of Estrogen receptor positive BRCA1-mutated breast cancer [human 3.5k BAC array]

first: Esther

last: Lips

address: Plesmanlaan 121

department: Molecular Pathology

institute: NKI-AVL

summary:
Purpose:
As estrogen receptor (ER)-positive breast cancer in BRCA1 mutation carriers arises at an older age with less aggressive tumor characteristics than ER negative BRCA1 mutated breast cancer, it has been suggested that these tumors are ?sporadic? and not BRCA1-driven. With the introduction of targeted treatments specific for tumors with a non-functioning BRCA1 or BRCA2 gene, the question whether the BRCA genes are impaired in the tumor, is highly relevant. Therefore, we performed genomic profiling of BRCA1-mutated ER+ tumors.

Experimental design:
Genomic profiling, BRCA1 promoter methylation assessment, and loss of heterozygosity analysis were done on 16 BRCA1-mutated ER+ tumors. Results were compared with 57 BRCA1-mutated ER- tumors, 36 BRCA2-mutated ER+ associated tumors, and 182 sporadic ER+ tumors  [GSE9021, GSE9114, GSE16511, GSE50407].

Results:
The genomic profile of BRCA1-mutated ER+ tumors was different from BRCA1-mutated ER- breast tumors, but highly similar to BRCA2-mutated ER+ tumors. In 83% of the BRCA1-mutated ER+ tumors, loss of the wildtype BRCA1 allele was observed. In addition, clinico-pathological variables in BRCA1-mutated ER+ cancer were also more similar to BRCA2-mutated ER+ and sporadic ER+ breast cancer than to BRCA1 mutated ER- cancers.

Conclusions:
As BRCA1-mutated ER+ tumors show a BRCAness copy number profile and LOH, it is likely that the loss of a functional BRCA1 protein plays a role in tumorigenesis in BRCA1-mutated ER+ tumors. Therefore, we hypothesize that these tumors are sensitive to drugs targeting the BRCA1 gene defect, providing new targeted treatment modalities for advanced BRCA-deficient, ER-positive breast cancer.

overall_design: This submission includes the data of 3 Estrogen receptor positive BRCA1-mutated breast cancers

middle: H

first: Rashmie

last: Debipersad

last: Scheerman

first: Lennart

last: Mulder

first: Gabe

last: Sonke

first: Lizet

last: van der Kolk

first: Jelle

last: Wesseling

first: Frans

last: Hogervorst

first: Petra

middle: M

last: Nederlof


title: Genomic profiling of Estrogen receptor positive BRCA1-mutated breast cancer [Nimblegen human 135K]

summary:
Purpose:
As estrogen receptor (ER)-positive breast cancer in BRCA1 mutation carriers arises at an older age with less aggressive tumor characteristics than ER negative BRCA1 mutated breast cancer, it has been suggested that these tumors are ?sporadic? and not BRCA1-driven. With the introduction of targeted treatments specific for tumors with a non-functioning BRCA1 or BRCA2 gene, the question whether the BRCA genes are impaired in the tumor, is highly relevant. Therefore, we performed genomic profiling of BRCA1-mutated ER+ tumors.

Experimental design:
Genomic profiling, BRCA1 promoter methylation assessment, and loss of heterozygosity analysis were done on 16 BRCA1-mutated ER+ tumors. Results were compared with 57 BRCA1-mutated ER- tumors, 36 BRCA2-mutated ER+ associated tumors, and 182 sporadic ER+ tumors [GSE9021, GSE9114, GSE16511, GSE50407]

Results:
The genomic profile of BRCA1-mutated ER+ tumors was different from BRCA1-mutated ER- breast tumors, but highly similar to BRCA2-mutated ER+ tumors. In 83% of the BRCA1-mutated ER+ tumors, loss of the wildtype BRCA1 allele was observed. In addition, clinico-pathological variables in BRCA1-mutated ER+ cancer were also more similar to BRCA2-mutated ER+ and sporadic ER+ breast cancer than to BRCA1 mutated ER- cancers.

Conclusions:
As BRCA1-mutated ER+ tumors show a BRCAness copy number profile and LOH, it is likely that the loss of a functional BRCA1 protein plays a role in tumorigenesis in BRCA1-mutated ER+ tumors. Therefore, we hypothesize that these tumors are sensitive to drugs targeting the BRCA1 gene defect, providing new targeted treatment modalities for advanced BRCA-deficient, ER-positive breast cancer.

overall_design: This submission includes the data of 13 Estrogen receptor positive BRCA1-mutated breast cancers

middle: E


title: Genomic profiling of Estrogen receptor positive BRCA1-mutated breast cancer

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

overall_design: Refer to individual Series


title: gravitropic stimulation / isotropic light-Characterization of early molecular events of woody stem gravitropism independently of phototropic responses

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

summary: 12plex_poplar_2012-01 - gravitropic stimulation / isotropic light - The experiments were designed to identify genes responding to the gravitropic stimulus in the xylem of poplar stem independently of phototropic responses. - young poplar trees were staked one week before use. For the experiment, the plants were placed in an isotropic light environment and were tited at 35° during 30 min. Control plants were kept straight in the isotropic light device. Xylem samples were collected from the upper and lower face of the stems. 4 biological replicates were made (4 controls and 4 tilted plants). RNA was extracted from each xylem sample. cDNA was synthetized. The discovery of genes whose expression is modulated by tilting was performed by a microarray approach.

overall_design: 8 dye-swap - treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Patricia-

last: Roeckel-drevet

first: Marie-Laure

last: Martin-Magniette


title: Overlapping and antagonistic genes affected in the sdg8, sdg26 and sdg8 sdg26 mutants

first: Ying

last: Ruan

address: No.1 YuanDa Road

department: College of Bioscience and Biotechnology

summary: To evaluate the role of SDG8 and SDG26 in genome transcription, we performed transcriptome analyses using 6-day-old seedlings and identified differentially expressed genes in the sdg8, sdg26 and sdg8 sdg26 mutants as compared to wild-type(Col).

overall_design: Seedlings of wild type control(Col) vs. Mutant sdg8,sdg26 and sdg8 sdg26. Based on two independent experiments obtained each with three independently derived sets of RNA for each genotype.

first: Wen-Hui

last: Shen

first: Boyu

last: Liu

first: Alexandre

last: Berr


title: Exposure of Campylobacter jejuni to acid stress enhances its pathogenesis and cross-protects the bacterium against other stresses

city: ottawa

first: ALAIN

last: STINTZI

state: ONTARIO

address: 451 SMYTH ROAD

department: BIOCHEMSISTRY, MICROBIOLOGY AND IMMUNOLOGY

institute: UOTTAWA

summary:
Campylobacter jejuni is the prevalent cause of bacterial gastroenteritis in human worldwide. The ability to survive stomach acidity is a fundamental requirement for C. jejuni to colonize the host and cause disease. However, the mechanism of C. jejuni acid survival is still unknown. Herein, we demonstrated that C. jejuni is able to survive acidic conditions at pH 4 up to 8 min without a drop in viability. The acid stimulon of C. jejuni 81-176 revealed the up-regulation of many genes important for Campylobacter acid survival such as heat shock genes and genes involved in energy metabolism. On the other hand, the repression of ribosomal genes highlights the ability of C. jejuni to direct its machinery to survive stressful conditions. Prior acid exposure cross-protected C. jejuni against oxidative stress suggesting an overlap in C. jejuni’s responses to various stresses. Interestingly, the induced expression of virulence genes in C. jejuni upon acid exposure such as the Campylobacter invasion antigen (ciaB) indicates that acid stress plays a role in C. jejuni host pathogenesis. Acid exposure significantly enhanced C. jejuni pathogenesis in both eukaryotic cells and G. melonella. To the best of our knowledge, this is the first study characterizes the influence of acid stress on C. jejuni pathogenesis in an infection model. Altogether, this study uncovers the transcriptional profile of C. jejuni in response to acidic conditions as those encountered in the stomach. In addition, our results demonstrate that acid stress jump-starts C. jejuni for efficient gut colonization and host pathogenesis.
Campylobacter jejuni is the prevalent cause of bacterial gastroenteritis in human worldwide. The ability to survive stomach acidity is a fundamental requirement for C. jejuni to colonize the host and cause disease. However, the mechanism of C. jejuni acid survival is still unknown. Herein, we demonstrated that C. jejuni is able to survive acidic conditions at pH 4 up to 8 min without a drop in viability. The acid stimulon of C. jejuni 81-176 revealed the up-regulation of many genes important for Campylobacter acid survival such as heat shock genes and genes involved in energy metabolism. On the other hand, the repression of ribosomal genes highlights the ability of C. jejuni to direct its machinery to survive stressful conditions. Prior acid exposure cross-protected C. jejuni against oxidative stress suggesting an overlap in C. jejuni’s responses to various stresses. Interestingly, the induced expression of virulence genes in C. jejuni upon acid exposure such as the Campylobacter invasion antigen (ciaB) indicates that acid stress plays a role in C. jejuni host pathogenesis. Acid exposure significantly enhanced C. jejuni pathogenesis in both eukaryotic cells and G. melonella. To the best of our knowledge, this is the first study characterizes the influence of acid stress on C. jejuni pathogenesis in an infection model. Altogether, this study uncovers the transcriptional profile of C. jejuni in response to acidic conditions as those encountered in the stomach. In addition, our results demonstrate that acid stress jump-starts C. jejuni for efficient gut colonization and host pathogenesis.

overall_design: Three biological with three technical replicates for both test and control samples

first: Momen

last: Askoura

first: Alain

last: Stintzi


title: Transcriptional Profiles in Bursal B-Lymphoid DT40 Cells Infected with Very Virulent Infectious Bursal Disease Virus

city: Beijing

first: Rong

last: Quan

address: No. 9 Shuguang Garden Middle Road, Haidian District

institute: Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences

summary: Infectious bursal disease virus (IBDV) causes a highly contagious, immunosuppressive disease in chickens. The virus mainly infects immature B lymphocytes in the bursa of Fabricius (BF). Chicken B cell line DT40, an avian leukosis virus-induced B cell line, supports very virulent IBDV (vvIBDV) infection in vitro and thereby serves as a good model for investigating the infection and pathogenesis of this virus. However, a transcriptome-wide understanding of the interaction between vvIBDV and B cells has not yet been achieved. This study aimed to employ time-course DNA microarrays to investigate gene expression patterns in DT40 cells after infection with vvIBDV strain LX.

overall_design: 6 samples.including DT40 cells infected with vvIBDV strain LX at an MOI of 5 EID50 and collected at the 12, 18, 24, 36, 48 hours post-infection (pi) and mock ones.

first: Shanshan

last: Zhu

first: Jue


title: 09 Chemical-induced gene expression changes in rat liver

status: Public on Sep 30 2016

city: Kitakatsushika-gun

first: Kyosuke

last: Yamashita

state: Saitama

address: Sugito-machi Shimotakano1600

department: Tokyo

institute: Chemicals Evaluation and Research Institute Japan

summary: 2,2-Bis(Bromomethyl)-1,3-Propanediol-induced gene expression changes in rat liver

overall_design: Gene expression in rattus norvegicus liver was measured at 28 days.

first: Hiroshi

last: Matsumoto

first: Fumiyo

last: Saito

first: Masahiro

last: Takeyoshi


title: 10 Chemical-induced gene expression changes in rat liver

summary: Nitrilotriacetic acid trisodium monohydrate-induced gene expression changes in rat liver


title: PHGR1 knockdown in the colorectal cell line HT29

city: Stavanger

first: Oddmund

last: Nordgard

address: Gerd Ragna Bloch Thorsens gate 8

department: Dep. of Hematology and Oncology

institute: Stavanger University Hospital

summary:
HT29 cells were transfected with two different PHGR1-targeted siRNA and a scramble siRNA (control) in four copies. Global mRNA profiling was performed by hybridization to
Illumina Human-6 Express BeadChips (version 2). Genes significantly up- or downregulated for both PHGR1-targeted siRNAs were identified.

overall_design:
The transfections and corresponding hybridizations were done in four parallelles (12 samples in total). The controls were HT29 cells transfected with a scramble siRNA.
Probe-level data not available.


title: 08 Chemical-induced gene expression changes in rat liver

summary: Tris(2-Chloroethyl) Phosphate hydrochloride-induced gene expression changes in rat liver


title: 07 Chemical-induced gene expression changes in rat liver

summary: o-Anthranilic acid-induced gene expression changes in rat liver


title: Chemical-induced gene expression changes in rat liver


title: 06 Chemical-induced gene expression changes in rat liver

summary: tert-Butyl alcohol-induced gene expression changes in rat liver


title: 03 Chemical-induced gene expression changes in rat liver

summary: 1-Amino-2,4-Dibromoanthraquinone-induced gene expression changes in rat liver


title: 04 Chemical-induced gene expression changes in rat liver

summary: N-Nitrosodimethylamine-induced gene expression changes in rat liver


title: 02 Chemical-induced gene expression changes in rat liver


title: 01 Chemical-induced gene expression changes in rat liver

summary: Bromodichloromethane-induced gene expression changes in rat liver


title: Expression data from adult zebrafish exposed to low level TCDD

city: Gainesville

first: Tracie

middle: R

last: Baker

state: FL

institute: University of Florida

summary:
Exposure to TCDD early in development produces reproductive abnormalities in adulthood and decreased reproductive capacity in males
We used microarrays to investigate the global programme of gene expression in testicular tissue and identified distinct gene expression changes due to TCDD exposure in males.

overall_design: Zebrafish were exposed to sublethal TCDD or vehicle (DMSO) during early development and analyzed for phenotypic and gene expression changes as adults. 5 TCDD and 5 Control males.


title: Transcriptomic profiling of engineered and improved Saccharomyces cerevisiae for xylose utilization

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

summary: The aim of present study is to understand the impact of xylose utilization on the  Saccharomyces cerevisiae physiology after initial genetic engineering and in a strain with an improved xylose utilization phenotype.

overall_design: A twenty four array study using total RNA recovered from xylose-utilizing Saccharomyces cerevisiae yeast strains M6880 and M7237 grown in chemostat culture.

first: Steven

middle: D

last: Brown

first: Sean

last: Covalla

first: Allan

last: Froehlich


title: Effect of post-ruminal butyrate infusion on gene expression in the duodenum of growing sheep

city: Clay Center

first: Andrew

middle: P

last: Foote

state: NE

address: PO Box 166

department: NEMRU

institute: US Meat Animal Research Center

summary: Objectives were to determine the effect of supplying butyrate post-ruminally on gene expression in the duodenum of growing polled Dorset lambs.

overall_design: The transcriptome of the duodenum from 9 lambs were examined for expression differences in response to butyrate infusion into the abomasum.


title: Microenvironment Cell Populations

status: Public on Sep 02 2016

city: Seattle

first: Etienne

last: Becht

address: 1100 Fairview Ave N

institute: Fred Hutchison Cancer Research Center

type:
Expression profiling by array
Third-party reanalysis

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


title: Human somatic cells subjected to genetic reprogramming with germ line-related factors show meiotic germ cell-like features

city: Valencia

first: Jose

middle: Vicente

last: Medrano

state: Valencia

address: Avenida Fernando Abril Martorell, 106

department: Reproduction Unit

institute: IIS La Fe

summary: Results from expression arrays identified that whole cultures of i12F-reprogrammed fibroblasts clustered in a defined group and indicated a switch in their genetic expression program, as shown by the significant up-regulation of 342 genes and the down-regulation of 288 genes in treated cells compared to MOCK controls. Manually isolated i12F clumps also clustered in a defined group different to i12F and showed significant up-regulation of 329 genes (193 of them shared with i12F treatment) and down-regulation of 372 genes (225 of them shared with i12F treatment) compared to MOCK controls (Fig. 1B). Functional enrichment analysis of the list of differentially regulated genes in i12F indicated their implication in germ cell-related processes such as “Integrin cell surface interactions” (REACT_13552), “Cell cycle” (REACT_152), “DNA Replication” (REACT_383), “Telomere maintenance (REACT_7970), as well as several Gene Ontology biological processes related to “Positive regulation of MAP kinase activity” (GO:0043406), “ovarian follicle development” (GO:0001541), “positive regulation of tyrosine phosphorylation of STAT protein” (GO:0042531), “Retinoid acid metabolic process” (GO:0042573) and “transforming growth factor beta receptor signaling pathway” (GO:0007179), among others. Interestingly, we observed the significant down-regulation of several genes related to the mitotic cell cycle regulation such as CDC45L, RRM2, CDKL2, CENPM, CENPP, ZWINT, PRKAR2B, PKMYT1, SKA3, ADORA2B, CDCA8, CDC6, BUB1 and LIG1, and the significant up-regulation of genes related to the TGFβ and LIF/STAT3 pathways such as INHBA, IL6, CSF2 and MAFB, and cell attachment to basal layer such as ITGA1, MMP9 and MMP10. On the other hand, we observed a specific significant down-regulation in the CLUMPS of several genes related to chromatin stability such as the linker histone 1 subunits H4B, H4H, H4K, H2AB and H3J, the core histone 2 subunits H2AA4 and H4B, and several somatic lineage determinant factors such as GATA2, NEUROD2 and SOX17. Aditionally we observed a significant up-regulation of extracellular matrix related genes such as ADAM8 and MMP14, and the pathway of LIF/STAT3

overall_design: RNA samples from 14 days post-transduction cultures were analyzed with the Whole Human Genome Oligo Microarray (Agilent GE 4 × 44K Human v2 microarrays, Agilent Technologies).

middle: V


title: Gene expression in granulosa cells from cows rated as poor donors of competent oocytes

city: Quebec

first: David

middle: André

last: Landry

state: Quebec

address: 2440 boul. Hochelaga

department: Animal Science

institute: University Laval

summary: The objective of this study was to gain better understanding of the follicular conditions associated with low oocyte developmental competence. In summary, we demonstrated that differences in follicle maturity at collection could explain differences in oocyte competence associated with individual animals. We also revealed deficiencies in lipid metabolism and retinol signalling in granulosa cells from donors of mostly incompetent oocytes.

overall_design: Granulosa cells from 94 Holstein cows in a commercial embryo production facility were collected following ovarian stimulation and coasting, to compare gene expression from donors of mostly competent versus incompetent oocytes

middle: A

first: Anne-Marie

last: Bellefleur

first: Rémi

last: Labrecque

first: François-Xavier

last: Grand

first: Christian

last: Vigneault

first: Patrick

last: Blondin

first: Marc-André

last: Sirard


title: ADDITIVE EFFECTS OF MILLIMETER WAVES AND 2 DEOXYGLUCOSE CO-EXPOSURE ON THE HUMAN KERATINOCYTE TRANSCRIPTOME

status: Public on Sep 20 2016

city: Fougeres

first: Denis

last: Habauzit

address: 10 B rue Claude Bourgelat

department: TC unit

institute: ANSES

summary: To evaluate the effect of millimeter waves (MMW) exposure on the gene expression, we have employed whole genome microarray expression profiling. Neonatal primary Keratinocyte cells pooled from 3 healthy donors were exposed ex vivo, by 60.4 GHz-MMW, at an incident power density (IPD) of 20 mW/cm² (3 hours of treatment in athermic condition).No modification of keratinocyte transcriptome was observed. Considering that MMW could also impact the cell metabolism, we assessed then effect of glycolysis inhibitor 2 deoxyglucose treatment (2dG, 20 mM during 3 hours) in association with MMW co-exposure. 2dG treatment induces a high modification of the transcriptome (632 coding genes). Genes affected in their expression are linked with transcriptional repression, cellular communication and endoplasmic reticulum homeostasis. The MMW/2dG co-exposition induced a slight modification of cell transcriptome, which reflects the capacity of MMW to interfere with bioenergetic stress response. After RT-PCR validation, 6 genes (SOCS3, SPRY2, TRIB1, FAM46A, CSRNP1 and PPP1R15A) were confirmed as sensitive to MMW exposure during 2dG treatment.

overall_design: Gene expression in human keratinocytes was measured after a 60 GHz-exposure at 20 mW/cm2, for 3 h (Expo). It was compared to cells cultured in unexposed condition (Sham). As millimeter wave (MMW) exposure impact on metabolism we assessed then effect of glycolysis inhibitor 2 deoxyglucose treatment (2dG, 20 mM during 3 hours: Sham_2dG) in association with MMW co-exposure (Expo_2dG).

first: Yonis

last: Mahamoud

first: Meziane

last: Aite

first: Catherine

last: Martin

first: Maxim

last: Zhadobov

first: Ronan

last: Sauleau

first: Yves

last: Le Dréan


title: Exosomal microRNA, miR-1246, induces cell motility and invasion through the regulation of DENND2D in oral squamous cell carcinoma

status: Public on Aug 15 2016

city: Tokyo

first: Tomoki

last: Muramatsu

address: 1-5-45 Yushima Bunkyo-ku

department: Medical research institute

institute: Tokyo Medical and Dental University

summary:
To Identify of metastasis-related genes and metastasis-related miRNA in oral squamous cell carcinoma by miRNA profiling of HOC313-Parent, HOC313-LM and their respective exosomes carried out. As a result, miR-342-3p and -1246 were found candidate oncogenic miRNAs.
To further identify the  target genes of miR-1246 and miR-342-3p, we performed gene expression array analysis with HOC313-LM and HOC313-Parent (HOC313-P) transfected NT, miR-342-3p and miR-1246. Moreover, to identify tumor suppressor genes, gene expression profiles of each of transfected cells and HOC313-LM cells were analyzed by in silico analyses.  As a result, DENND2D emerged as the possible target of miRN-1246.

overall_design: Extraction of difference of miRNA expression level between whole cell and exosomes of HOC313-Parent and HOC313-LM.  Also, extraction of difference of gene expression level between high-metastatic subline (HOC313-LM) and low-metastatic subline (HOC313-P). Moreover the miRNA expression profiles and gene expression profiles were analyzed by in silico analyses.

first: Sujata

last: Sakha

first: Johji

last: Inazawa


title: Multi-scale genomic, transcriptomic and proteomic analysis of colorectal cancer cell lines to identify novel biomarkers

status: Public on Aug 23 2016

city: Edinburgh

first: Romina

last: Briffa

state: Lothian

address: Crewe Road South

department: Division of Pathology

country: United Kingdom

institute: University of Edinburgh

summary: The objective of this study was to measure copy number alterations in a panel of 15 CRC cell lines and relate them to treatment sensitivity.

overall_design: Assessment of copy number variations in a panel of 15 colorectal cancer cell lines

first: Charlene

last: Kay

first: Morad

last: Ansari


title: 05 Chemical-induced gene expression changes in rat liver

first: Kyosuke

last: Yamashita

summary: Phenolphthalein-induced gene expression changes in rat liver

first: Hiroshi

last: Matsumoto

first: Fumiyo

last: Saito

first: Masahiro

last: Takeyoshi


title: Gene expression during metabolism of sugars by Alicyclobacillus acidocaldarius

status: Public on Aug 31 2016

city: Richland

first: Brady

last: Lee

state: Washington

address: 902 Battelle Boulevard

country: USA

institute: Pacific Northwest National Laboratory

summary: The purpose of this study was to characterize carbon metabolism and gene regulation in Alicyclobacillus acidocaldarius during growth on monosaccharides in an effort to determine whether carbon catabolite repression was active.  Chemostat studies and global transcriptome analysis were used to accomplish this goal.

overall_design: A six chip study using total RNA recovered from three sets of triplicate chemostat experiments using Alicyclobacillus acidocaldarius ATCC27009/DSM446 growing using xylose and glucose, fructose and glucose or xylose and arabinose.  Each chip measures the expression level of 3,554 genes from Alicyclobacillus acidocaldarius ATCC27009/DSM446 with seven 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: William

last: Apel

first: Linda

last: DeVeaux

first: Peter

last: Sheridan


title: Expression of mRNA from lung tissue from Systemic Sclerosis patients with interstitial lung disease (SSc-ILD)  and healthy controls (HC)

status: Public on Aug 01 2016

city: Boston

first: Romy

middle: B

last: Christmann

state: MASSACHUSETTS

address: 715 Albany Street E5

institute: Boston University School of Medicine

summary:
Objective: MicroRNAs (miRNAs) control key elements of mRNA stability and likely contribute to the dysregulated lung gene expression observed in systemic sclerosis associated interstitial lung disease (SSc-ILD). We analyzed the miRNA gene expression of tissue and cells from SSc-ILD patients. A chronic lung fibrotic murine model was used.
Methods: RNA was isolated from lung tissue of 12 SSc-ILD patients and 5 control lungs. High-resolution computed tomography (HRCT) was performed at baseline and 2-3 years after treatment. Lung fibroblasts and PBMCs were isolated from healthy controls and SSc-ILD patients. miRNA and mRNA were analyzed by microarray, quantitative polymerase chain reaction, and/or Nanostring; pathway analysis was performed by DIANA-miRPath v2.0 software. Wild-type and miR-155 deficient (miR-155ko) mice were exposed to bleomycin.
Results: Lung miRNA microarray data distinguished patients with SSc-ILD from healthy controls with 185 miRNA differentially expressed (q<0.25). DIANA-miRPath revealed 57 KEGGs pathways related to the most dysregulated miRNAs. miR-155 and miR-143 were strongly correlated with progression of the HRCT score. Lung fibroblasts showed only mild expression of miR-155/miR-21 after several stimuli. miR-155 PBMC expression strongly correlated with lung function tests in SSc-ILD. miR-155ko mice developed milder lung fibrosis,  survived longer, and showed a weaker lung induction of several genes after bleomycin exposure compared to wild-type mice.
Conclusions: miRNAs are dysregulated in lungs and PBMCs of SSc-ILD patients. Based on mRNA-miRNA interaction analysis and pathway tools, miRNAs may play a role in the progression of the disease. Our findings suggest that targeting miR-155 might provide a novel therapeutic strategy for SSc-ILD.

overall_design: Lung biopsies taken from open lung biopsy from SSc-ILD patients (n=15 samples) and from cancer free control patients (n=5) during ressection of the lung tumor.

first: Percival

last: Sampaio-Barros


title: Peripheral blood gene expression as a biomarker for early detection of Alzheimer’s disease

status: Public on Aug 11 2016

city: Shah Alam

first: Ainon

middle: Zahariah

last: Samsudin

state: Selangor

address: Bandar Puncak Alam

institute: University Teknologi Mara

summary: To further development of our gene expression profile of Alzheimer's disease, we have employed whole genome microarray expression profiling as a discovery platform to   identify genes with the potential biomarker for early disease detection

overall_design: Total RNA from peripheral blood cells was extracted, reverse-transcribed and labelled, then analysed for gene expression using GeneSpring GX12 (Agilent Technologies, USA). About 180 samples (AD=90, Non-demented control=90) was used for microarray analysis.

middle: Z

first: Abu Bakar

last: Abdul Majeed

first: Kalavathy

last: Ramasamy


title: Endothelial matrix-metalloproteinase-10 promotes pulmonary arterial hypertension associated with systemic sclerosis

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary:
Pulmonary endothelial dysfunction plays an integral role in mediating the initiation and progression of pulmonary vascular remodelling, an important feature of pulmonary arterial hypertension (PAH). Our aim was to decipher the gene expression program of endothelial cells derived from circulating endothelial progenitor (EPCs) to gain insight into the pathological process of PAH associated with systemic sclerosis (SSc), which is the most extreme vascular phenotype of this disease.
We used microarrays to investigate the gene expression profile in late outgrowth EPC-derived endothelial cells issued from SSc-PAH patients, in comparison with SSc patients without PAH and healthy controls.

overall_design: EPC-derived endothelial cells were isolated from peripheral blood of PAH-SSc patients, SSc patients without PAH and healthy control for RNA extraction and hybridization on Affymetrix microarrays. Gene expression profiles of EPC-derived endothelial cells were determined in basal conditions and also after hypoxic exposure.

first: Jérôme

last: Avouac

first: Yannick

last: Allanore