title: Expression data from transfection of two different antisense oligonucleotides in HuH7 cells

status: Public on Apr 21 2017

city: Horsholm

first: Peter

middle: H

last: Hagedorn

state: Danmark

address: Fremtidsvej 3

department: Research

country: Denmark

institute: Roche Innovation Center Copenhagen A/S

summary: We used microarrays to globally profile the gene expression changes observed after 24h when transfecting antisense oligonucleotides in HuH77 cells

overall_design: Two different antisense oligonucleotides, denoted SPC3302 (n=3) and SPC3833 (n=3), were transfected into HuH7 cells and gene expression changes relative to mock-treated controls (n=3) were measured by microarray after 24h.


title: HCC Cell lines: MHCC97L vs. Huh7 and HCCLM3

status: Public on Apr 12 2017

city: Tianjin

first: Yongmei

last: Li

address: No.22, Qixiangtai Road, Heping District

country: China

institute: Tianjin Medical University

summary: To identify genes associated with HCC invasiveness and metastasis, a hybridization-based microarray assay was used to analyze three cell lines with increasing metastatic potentials, Huh7,MHCC97L, and HCCLM3

overall_design: Three-condition experiment, MHCC97L vs. Huh7 and HCCLM3 cells. Biological replicates:3 replicates (each cell line) .

first: Ning

last: Zhang


title: Expression changes in L4 DRG initiated by sciatic nerve injury

status: Public on Apr 26 2017

city: South San Francisco

first: Kevin

last: Huang

state: California

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech

summary:
Expression of L4 DRG after sciatic nerve cut compared to contralateral uninjured DRGs.

The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0003322

Keywords: Expression profiling by array

overall_design: Microarray analysis of L4 DRGs 3 days after sciatic nerve transection in adult mice using uninjured DRGs as control.

first: Genentech

last: Inc.


title: TLR signaling in C57BL/6J TLR2,4,7-tolerant splenocytes over PBS-treated counterpart.

city: Thessaloniki

first: Nikolaos

last: Zogas

address: Exokhi

department: Hematology-BMT Unit

country: Greece

institute: George Papanicolaou Hospital

summary: Murine splenocytes were isolated from the spleens of C57BL/6J mice and were pretreated in vitro for three days in the presence of Pam3CSK4 (1 μg/ml), high pure LPS from E.coli O111:B4  (100 ng/ml) and R848 (5 μg/ml). PBS-treated splenocytes served as negative control. We used Qiagen Toll-like Receptor RT2 Profiler PCR Array kit to quantitate gene expression profiling of the TLR signaling pathway.

overall_design: qPCR gene expression profiling.  Splenocytes from 6 mice were used and treated separately as indicated in the summary. Equal amount of total cDNA from each mouse (reverse-transcribed from 0.5 μg RNA) was used prior to gene expression analysis.

first: Evangelia

last: Yannaki


title: Selection of yeast Saccharomyces cerevisiae promoters available for xylose cultivation and fermentation

status: Public on Apr 11 2017

city: Kobe

first: Akihiko

last: Kondo

address: 1-1 Rokkodai, Nada

department: Chemical Science and Engineering

country: Japan

institute: Kobe University

summary: To select candidate promoters that function in the presence of xylose, we performed comprehensive gene expression analyses using xylose-utilizing yeast strains both during xylose and glucose fermentation.

overall_design: Samples were taken after 9 h in fermentation medium containing 50g /L xylose or after 3 h in fermentation medium containing 50 g/L glucose, respectively. Each samples were triplicated resulting in total of 6 samples.

first: Yumiko

last: Nambu-Nishida

first: Yuri

last: Sakihama

first: Jun

last: Ishii

first: Tomohisa

last: Hasunuma


title: Effect of lipopolysachharide (LPS) on the expression of microRNAs (miRNAs) in the mouse oviduct

status: Public on Apr 14 2017

city: Lexington

first: Phillip

middle: J

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

summary: Our objective was to determine the effect of intraperitoneal (IP) administration of E. Coli-derived lipopolysaccharide (LPS) on the acute expression of miRNAs in the mouse oviduct

overall_design: On the day of estrus, 6-8 week old CD1 mice were treated IP with 0 (control), 2 µg (low dose) or 10 µg (high dose) of LPS from E. Coli serotype 055:B5 in 100 μL PBS.  Mice were killed 24 h later and the oviducts collected for determination of the effect of treatment on miRNAs (n=4/treatment) using the nCounter Mouse v.1.5 miRNA Expression Assay (Nanostring Technologies).  The effect of LPS on the expression of miRNAs was evaluated by one-way ANOVA and treatment means of differentially expressed miRNA (P<0.05) were separated using a post-hoc LSD test.

first: Katheryn

middle: L

last: Cerny

first: Rosanne

middle: A

last: Ribeiro


title: Effect of lipopolysachharide (LPS) on the expression of inflammatory mRNAs in the mouse oviduct

summary: Our objective was to determine the effect of intraperitoneal (IP) administration of E. Coli-derived lipopolysaccharide (LPS) on the acute expression of inflammatory mRNAs in the mouse oviduct

overall_design: On the day of estrus, 6-8 week old CD1 mice were treated IP with 0 (control), 2 µg (low dose) or 10 µg (high dose) of LPS from E. Coli serotype 055:B5 in 100 μL PBS.  Mice were killed 24 h later and the oviducts collected for determination of the effect of treatment on inflammatory mRNAs (n=4/treatment) by a targeted nanostring approach using the nCounter GX Mouse Inflammation Kit (Nanostring Technologies, Seattle, WA).  Real-time PCR was then used to verify a selection of mRNAs.  The effect of LPS on the expression of mRNAs was evaluated by one-way ANOVA and treatment means of differentially expressed mRNA (P<0.05) were separated using a post-hoc LSD test.


title: Effect of a salt restriction diet on cardiac damage in a rat model of metabolic syndrome

status: Public on Apr 20 2017

city: Montpellier

first: Caroline

last: DESMETZ

address: 15 avenue Charles Flahault

department: Faculty of pharmacy

country: France

institute: Montpellier University

summary:
We wanted to understand how a salt restriction diet could improve cardiac damage (ie cardiac hypertrophy, fibrosis, hypertension) in a rat model of metabolic syndrome.
We thus performed an Agilent microarray experiment in order to identify expression variations in left ventricles of rats having a normal sodium diet (0,64%) or a low sodium diet (less than 0,01%)

overall_design: Sprague-Dawley rats were fed for 8 weeks 60% fructose diet with either a normal sodium (0.64% NaCl) or a low sodium content (<0.01% NaCl) (n=40 in each). After 4 weeks, rats were infused or not with angiotensin II (200 ng.kg-1.min-1, sc) for 4 weeks. At the end of the experiment, heart left ventricles were collected in RNA later for further mRNA extraction.

first: Bernard

last: Jover

first: Christelle

last: Reynes

last: Desmetz


title: Neonatal DNA methylation distinguishes children who will and will not become asthmatic by age 9 years

status: Public on Apr 13 2017

city: Tucson

first: Donata

last: Vercelli

state: Arizona

address: 1657 E. Helen Street

institute: University of Arizona

type: Methylation profiling by genome tiling array

summary:
Background   The timing and mechanisms of asthma inception remain imprecisely defined. Although epigenetic mechanisms likely contribute to asthma pathogenesis, little is known about their role in asthma inception.

Objective   To assess whether the trajectory to asthma begins already at birth and epigenetic mechanisms, specifically DNA methylation, contribute to asthma inception.

Methods   We used a combination of methyl binding protein-dependent DNA capture and microarrays to survey DNA methylation in cord blood mononuclear cells (CBMC) from 36 children (18 non-asthmatic, 18 asthmatic by age 9) from the Infant Immune Study (IIS), an unselected birth cohort closely monitored for asthma for a decade. SMAD3 methylation in IIS (n=60) and in two replication cohorts (The Manchester Asthma and Allergy Study, n=30, and the Childhood Origins of ASThma Study, n=28) was analyzed by bisulfite sequencing or Illumina 450K arrays. CBMC-derived IL-1b was measured by ELISA.

Results   Neonatal immune cells harbored 589 differentially methylated regions (DMRs) that distinguished IIS children who did and did not develop asthma by age 9. In all three cohorts, methylation in SMAD3, the most connected hub within the network of asthma-associated DMRs, was selectively increased in asthmatic children of asthmatic mothers and was associated with childhood asthma risk. Moreover, SMAD3 methylation in IIS neonates with maternal asthma was strongly and positively associated with neonatal production of IL-1b, an innate inflammatory mediator.

Conclusions   The trajectory to childhood asthma begins at birth and involves epigenetic modifications in immunoregulatory and pro-inflammatory pathways. Maternal asthma influences epigenetic mechanisms that contribute to the inception of this trajectory.

overall_design: CBMCs from children who did (n=18) or did not (n=18) become asthmatic by age 9 years


title: Biological processes induced by ZnO, Amoxicillin, and Rye in cultured Intestinal Porcine Epithelial Cells (IPEC-J2)

status: Public on Apr 19 2017

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

country: Netherlands

institute: Animal Sciences Group

summary: The objective of this study is to investigate to what extent gene expression data of dietary interventions generated in IPEC-J2 in vitro model overlap with in vivo data. Gene expression was recorded in IPEC-J2 cells upon exposure to three different dietary interventions commonly used in livestock. In a further step, we compared the results with mucosal gene expression responses, as measured in animals exposed to the same compounds via the diet. As compounds we used zinc oxide, rye and the antibiotic amoxicillin. The GEO accession numbers of the in vivo datasets are provided in the paper "Enrichment of in vivo determined transcription data from dietary intervention studies with in vitro data provides improved insight into gene regulation mechanisms" (submitted to "Genes and Nutrition").

overall_design:
IPEC-J2 cells were grown for 7 days at 37 ºC and 5% CO2 using 1:1 DMEM/Ham’s F10 1:1 medium supplemented with 5% FCS without antibiotics. For all tests, confluent monolayers were washed twice with medium without FCS (hereafter denoted as medium) and incubated for 1 hour with this medium. Hereafter, the medium was discarded and an additive dissolved/suspended in medium was added. Concentrations of 2.5% w/v Amoxicillin (brand name Octacillin), 0.03125% w/v of ZnO, and of a 3-fold diluted suspension of the diets containing 0%, 5% or 10% w/v Rye in culture medium were used for incubation of IPEC-J2 monolayers for a period of 2 and 6h. All incubations were tested in duplicate and for each type of additive duplicate control wells containing no additive (only culture medium) were incubated for 2 and 6h. After incubation total RNA was extracted. Each duplicate incubation was hybridized separately on a microarray patch.
IPEC-J2 enterocyte cell line derived from the jejunum of piglets, host-feed interaction

middle: M

first: Arjan

last: Hoekman

first: Mari

last: Smits


title: Differential gene expression in the muscle tissue of crossbred beef cows with divergent gain after feed restriction and ad libitum feeding studies.

status: Public on Apr 24 2017

city: Clay Center

first: Amanda

middle: K

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

summary:
Beef cow muscle transcriptome
Evaluation of the naturally occurring transcriptome variation among beef cows with divergent gain.

overall_design: The transcriptome of muscle tissue obtained after feed restriction and ad libitun feed were examined for expression differences that contribute to body weight gain.

last: Lindholm-Perry

first: Hannah

middle: C

last: Cunningham


title: miRNA profiling in monocrotaline (MCT)-induced pulmonary arterial hypertension in mice

status: Public on Apr 15 2017

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

summary: The outcome of miRNAs were successfully constructed through a differential expression profiling of a total of 190 unique miRNA in MCT-treated mice compare to the wild-type (WT) mice.

overall_design: The present study designed for the first time to investigate miRNA profiling in MCT-treated mice in the development of pulmonary arterial hypertension. Untreated WT mice were used as comparative control.

first: Sudhiranjan

last: Gupta


title: Microarray expression profile and functional analysis of circular RNAs in osteosarcoma

city: Guangzhou

first: Weihai

last: Liu

state: Guangdong

address: 58 Zhongshan Road 2

department: Department of Musculoskeletal Oncology

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Seven human osteosarcoma cell lines (U2OS, U2OS/MTX300, HOS, MG63, 143B, ZOS, ZOSM) and the human osteoblast hFOB1.19 were included in the study. Microarray based circRNA expression profiles were acquired using the Arraystar Human circRNA Array (8x15K, Arraystar). We identified circRNAs differentially expressed in human osteosarcoma cell lines compared to human osteoblast hFOB1.19 (control).

overall_design: In the study presented here, the circRNA expression in human osteosarcoma cell lines was compared to circRNA expression in human osteoblast hFOB1.19 (control).

first: Junqiang

last: Yin


title: Maize endosperm vp1 mutant response to water deficit

city: Ithaca

first: Tim

middle: L.

last: Setter

state: NY

address: 517 Bradfield Hall

department: Crop & Soil Sci; Plant Breeding & Genetics

institute: Cornell University

summary:
The goal of this work was to identify transcripts in maize endosperm that are regulated by water stress and the transcription factor Vp1
Keywords: stress response

overall_design: Plants were grown from F1 hybrid seed produced from inbreds W22 and ACR5855, where both inbred parents contributed mutant vp1-R alleles.  Florets were fertilized with pollen from either homozygous vp1 pollen, thus creating vp1/vp1/vp1 mutant endosperms, or Vp1 pollen, thus creating Vp1/vp1/vp1 endosperms.  Water stress treatment was imposed by withholding irrigation at 5 days after pollination; endosperms were sampled at 10 d after pollination.  The study had 2 X 2 factorial design with two genotypes and two watering treatments; there were 6 biological replicates.

first: LongXi

last: Yu


title: Effects of rye inclusion in broilers

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

institute: Wageningen UR

summary: An experiment was conducted to investigate the effects of dietary inclusion of rye, a model ingredient to increase gut viscosity, between 14 and 28 days of age  on immune competence related parameters and performance of broiler. A total number of 960 one-day-old male Ross 308 chicks were weighed and randomly allocated to 24 pens (40 birds per pen), and the birds in every 8 replicate pens were assigned to one of three experimental diets including graded levels, 0%, 5%, and 10% of rye. Tested immune competence related parameters were composition of the intestinal microbiota, genes expression in gut tissue, and gut morphology. The inclusion of 5% or 10% rye in the diet (d14-28) resulted in decreased performance and litter quality, but in increased villus height and crypt depth in the small intestine (jejunum) of the broilers. Relative bursa and spleen weights were not affected by dietary inclusion of rye. In the jejunum, no effects on number and size of goblet cells, and only trends on microbiota composition in the digesta were observed. Dietary inclusion of rye affected expression of genes involved in cell cycle processes of the jejunal enterocyte cells, thereby influencing cell growth, cell differentiation and cell survival, which in turn were consistent with the observed differences in the morphology of the gut wall. In addition, providing rye-rich diets to broilers affected the complement and coagulation pathways, which are parts of the innate immune system. These pathways are involved in eradicating invasive pathogens. Overall, it can be concluded that inclusion of 5% or 10% rye to the grower diet of broilers had limited effects on performance. Ileal gut morphology, microbiota composition of jejunal digesta, and gene expression profiles of jejunal tissue, however, were affected by  dietary rye inclusion level, indicating that rye supplementation to broiler diets might affect immune competence of the birds.

overall_design: An experiment was conducted to investigate the effects of dietary inclusion of three levels (0, 5, and 10%) of rye between 14 and 28 days of age on gut health and performance in broilers. A total of 960 one-day-old male Ross 308 chicks were allocated to 24 pens (40 birds per pen). Here, each sample is a pool of chickens per pen (n=6) that were euthanised at day 14, 21, or 28.

first: Marinus

last: van Krimpen

first: Stephanie

last: Vastenhouw


title: TLR signaling in C57BL/6J TLR7-tolerant CD3+ T-cells over the unmanipulated state.

first: Nikolaos

last: Zogas

summary: Murine CD3+ T-cells were immunomagnetically purified from the spleens of C57BL/6J mice and were pretreated in vitro for three days in the presence of R848 (5 μg/ml). Unmanipulated T-cells served as negative control. We used Qiagen Toll-like Receptor RT2 Profiler PCR Array kit to quantitate gene expression profiling of the TLR signaling pathway.

overall_design: qPCR gene expression profiling.  CD3+ T-cells from 5 mice were used and treated separately as indicated in the summary. Equal amount of total cDNA from each mouse (reverse-transcribed from 0.5 μg RNA) was used prior to gene expression analysis.

first: Evangelia

last: Yannaki


title: A paternal methyl donor-rich diet altered cognitive and neural functions in offspring mice [MeDIP_chip]

city: Bonn

first: Dan

last: ehninger

address: Sigmund-Freud-Straße 27

country: Germany

institute: German Center for Neurodegenerative Diseases

summary:
Evaluation of transgenerational influence of paternal dietary methyl substrates on offspring and grand-offspring brain and behavior
Dietary intake of methyl donors, such as folic acid and methionine, shows considerable intra-individual variation in human populations. While it is recognized that maternal departures from the optimum of dietary methyl donor intake can increase the risk for mental health issues and neurological disorders in offspring, it has not been explored whether paternal dietary methyl donor intake influences behavioral and cognitive functions in the next generation. Here, we report that elevated paternal dietary methyl donor intake in a mouse model, transiently applied prior to mating, resulted in offspring animals (MD F1 mice) with deficits in hippocampus-dependent learning and memory, impaired hippocampal synaptic plasticity and reduced hippocampal theta oscillations. Gene expression analyses revealed altered expression of the methionine adenosyltransferase Mat2a and BK channel subunit Kcnmb2, which was associated with changes in Kcnmb2 promoter methylation in MD F1 mice. These phenomena did not extend into the F2 offspring generation. Together, our data indicate that paternal dietary factors influence cognitive and neural functions in the offspring generation.

overall_design: Adult male mice were given either a normal laboratory control diet or a methyl-donor supplement diet containing added folic acid, L-methionine, choline, zinc, betaine and vitamine B12 for 6 weeks prior to mating. Their sperm DNA methylation, as well as their offspring (and grand-offspring) hippocampal methylation was evaluated using MeDIP-chip

last: Ehninger

first: Brandon

last: Pearson


title: Comparative study of host response to chytridiomycosis in susceptible and resistant toad species

status: Public on Apr 18 2017

city: Berkeley

first: Thomas

last: Poorten

state: CA

address: 54 Mulford Hall

department: Environmental Science, Policy, and Management

institute: UC Berkeley

summary: In the past century, recently emerged infectious diseases have become major drivers of species decline and extinction. Amphibian declines have occurred due to the fungal disease chytridiomycosis, which has exacerbated the conservation crisis of this taxonomic group. Biologists are beginning to understand what traits are important for susceptibility to this disease, but more work is needed to determine why some species succumb to disease while others do not. We conducted a laboratory experiment to examine how two toad species respond to infection in controlled environment. We selected two related species thought to differ in susceptibility – Bufo marinus (an invasive and putatively resistant species) and B. boreas (an endangered and putatively susceptible species). We measured infection intensity, body weight, histological changes at the site of infection, and genome-wide gene expression changes using a custom assay developed from transcriptome sequencing. Our results confirmed that the two species differ in susceptibility. The more susceptible species, B. boreas, experienced higher infection intensities, loss in body weight, more dramatic histological changes, and larger perturbations in gene expression. We found key differences in skin expression responses in multiple pathways including up-regulation of skin integrity-related genes in the resistant B. marinus. Together our results show intrinsic differences in host response between related species, which are likely to be an important factor in explaining variation in response to a deadly emerging pathogen in wild populations.

sample_organism:
Rhinella marina
Anaxyrus boreas

platform_organism:
Xenopus tropicalis
Rhinella marina
Anaxyrus boreas

overall_design: We processed 72 tissue samples in total: six biological replicates, three tissue types (ventral skin, liver, spleen), two treatment groups (pathogen exposed, control), and two host species (Bufo marinus, Bufo boreas). The custom Nimblegen microarray design included 135,200 60-bp probes (excluding control probes) targeting 31,367 transcript contigs from Bufo marinus, Bufo boreas, and model species Xenopus tropicalis, with 4 probes per probe-set. We used the 12-plex microarray platform (12 arrays per glass slide). Differential expression analyses were performed separately for each tissue type and host species.

first: Erica

middle: B

last: Rosenblum


title: Fingerprinting of the hNGF P61R100E gene expression in rat Dorsal Root Ganglion detected by microarray analysis

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: Nerve Growth Factor (NGF) is being considered as a therapeutic candidate for Alzheimer's disease (AD) treatment, not merely as a long-lasting cholinergic maintainer  and neuroprotective agent but also as a direct anti-amyloidogenic factor. However, the development of a NGF-based therapy for neurodegenerative diseases is limited by the partial access of NGF to the brain and to its potent nociceptive actions in animals and humans. Indeed, NGF is involved in pain transmission and perception. The nociceptive activity of NGF is mediated through the activation of TrkA and p75NTR receptors on sensory nerve endings. Our group recently studied forms of NGF, mutated at residue R100, inspired by the human genetic disease HSAN V (Hereditary Sensory Autonomic Neuropathy Type V), which would allow increasing the dose of NGF without triggering pain. This “painless” hNGF hNGFP61S/R100E displays full neurotrophic and anti-amyloidogenic activities in neuronal cultures, and a reduced nociceptive activity in vivo, via a selective alteration of TrkA versus p75NTR binding and signaling. The molecular mechanism through which  pNGF reduces nociceptive activity has never been investigated, therefore we performed gene expression microarray analysis to investigated the effect of hNGF hNGFP61S/R100E delivery in rat Dorsal Root Ganglia.

overall_design: DRG cell cultures were stimulated for experimental procedures using either double mutant hNGFP61S/R100E (n=3 replicates), single mutant hNGFP61S (n=3 replicates) or hNGF wild type (n=2 replicates) at 100 ng/ml concentration for 5 days. At the end of this incubation period, media and cells were collected for RNA extraction and microarray analysis.

first: Cinzia

last: Severini

first: Pamela

last: Petrocchi Passeri

first: Maria

middle: T

last: Ciotti

first: Fulvio

last: Florenzano

first: Carla

last: Petrella

first: Francesca

last: Malerba

first: Bruno

last: Bruni

first: Mara

last: D’Onofrio

first: Rossella

last: Brandi

first: Roberta

last: Possenti

first: Pietro

last: Calissano

first: Antonino

last: Cattaneo


title: TLR signaling in PBMCs acquired from BALB/c mice (10 days post-BMT) after being transplanted with T-cell depleted bone marrow alone (BMTCD), or in combination with TLR2,4,7-tolerant splenocytes, over their PBS-pretreated counterparts.

first: Nikolaos

last: Zogas

summary: Murine splenocytes were isolated from the spleens of C57BL/6J mice and were pretreated in vitro for three days in the presence of PBS, Pam3CSK4 (1 μg/ml), high pure LPS from E.coli O111:B4  (100 ng/ml) and R848 (5 μg/ml). BALB/c irradiated recipients, were transplanted with T-cell depleted bone marrow alone, or with the aforementioned pretreated splenocytes, and 10 days after, PBMCs from all experimental groups were collected for TLR signaling pathway analysis.We used Qiagen Toll-like Receptor RT2 Profiler PCR Array kit to quantitate gene expression profiling of the TLR signaling pathway.

overall_design: qPCR gene expression profiling.  PBMCs from 5 mice were used and treated separately as indicated in the summary. Equal amount of total cDNA from each mouse (reverse-transcribed from 0.5 μg RNA) was used prior to gene expression analysis.

first: Evangelia

last: Yannaki


title: ppmax2 response to gr24-Strigopath/Physcomitrella patens

status: Public on Apr 22 2017

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: 4plex_physco_2014-05 - ppmax2 response to gr24 - How does the Ppmax2 moss mutant respond to Strigolactone (GR24)?  - Two moss genotypes are used: WT and the Ppmax2 mutant. Moss tissues are fragmented, then plated on medium (Petri dish with cellophane disks) and cultivated for 3 weeks. Moss tissues are then transfered for 6 hours on acetone-containing medium (control treatment, for WT and Ppmax2) or GR24 (1 microM, in acetone)-containing medium (for Ppmax2). After 6 hours, the moss tissues are collected, quickly forzen in liquid nitrogen. RNA are isolated using the Quiagen RNeasy Plant mini kit (including a RNase-free DNase treatment on column). Two similar experiments (T1 and T2) have been led.

overall_design: 4 dye-swap - genotype comparaison,normal vs transgenic comparaison,treated vs untreated comparison

first: Geraldine

last: Bonnard

first: Catherine

last: Rameau

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Sensitive detection of radiation-induced medulloblastomas after acute or protracted gamma ray exposures in Ptch1 heterozygous mice using a radiation-specific molecular signature

city: Inage-ku

first: Benjamin

middle: John

last: Blyth

state: Chiba

address: 4-9-1 Anagawa

department: Centre for Radiation Protection

institute: National Institute of Radiological Sciences

summary: Recent studies have further heightened awareness of the risk of radiation-induced cancer after diagnostic radiology imaging, in particular, brain cancer following childhood CT scans. One feature of Ptch1+/- mice is that they are sensitive to radiation-induced medulloblastomas (an embryonic cerebellar tumor) during a narrow time window centered on the days around birth. The dynamics of how dose-protraction interacts with such narrow windows of sensitivity in individual tissues is still unknown. Using medulloblastomas from irradiated Ptch1+/- mice on a hybrid C3H × C57BL/6 F1 background, we have previously shown that the alleles retained on chromosome 13 (which harbors the Ptch1 gene) reveal two major mechanisms of loss of the wildtype allele. The loss of parental alleles from the telomere extending up to or past the Ptch1 locus by recombination (spontaneous-type) accounts for almost all medulloblastomas in unirradiated mice, while tumors in irradiated mice often exhibited interstitial deletions which start downstream of the wildtype Ptch1 and extend up varying lengths towards the centromere (radiation-type). Here, Ptch1+/- mice were exposed to an acute dose of 0.1 or 0.5 Gy gamma rays in utero or postnatally, or the same radiation doses protracted over a 4-day period, and were monitored for medulloblastoma development. The results show dose-dependent and age-dependent induction of radiation-type tumors; that the size of the radiation-induced deletion differs with the dose-rate; and, that tumor latency may be related to the size of the deletion. The radiation signature allows for unique mechanistic insight into the action of radiation to induce DNA lesions with known causal relationship to a specific tumor type, particularly for doses and dose-rates more relevant to diagnostic radiology imaging and accidental exposure of populations to radiation.

overall_design: 29 medulloblastomas arising in Ptch1 heterozygous mice were analysed for DNA copy number changes by array CGH, using each mouse's ear DNA as a reference. The medulloblastomas are from three groups, an acute exposure of 500 mGy on PN1, a protracted exposure of 500 mGy from PN1 to PN4, and from an unirradiated mouse.

first: Chizuru

last: Tsuruoka


title: Transcription factor Interplay between LEAFY and APETALA1/ CAULIFLOWER during Floral Initiation

status: Public on Apr 28 2017

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD

summary: The transcription factors LEAFY (LFY) and APETALA1 (AP1)_together with the AP1 paralog CAULIFLOWER (CAL)_control the onRep_of flower development in a partially redundant manner. This redundancy is thought to be mediated_at least in part_through the regulation of a shared Rep_of target genes. However_whether these genes are independently or cooperatively regulated by LFY and AP1/CAL_is currently unknown. To better understand the regulatory relationship between LFY and AP1/CAL during floral initiation_we monitored the activity of LFY in the absence of AP1/CAL function. We found that the regulation of several known LFY target genes is unaffected by AP1/CAL perturbation_while others appear to require AP1/CAL activity. Furthermore_we obtained evidence that LFY and AP1/CAL control the expression of some genes in an antagonistic manner. Notably_these include key regulators of floral initiation such TERMINAL FLOWER1 (TFL1)_which had been previously reported to be directly repressed by both LFY and AP1. We show here that TFL1 expression is suppressed by AP1 but promoted by LFY. We further demonstrate that LFY has an inhibitory effect on flower formation in the absence of AP1/CAL activity. We propose that LFY and AP1/CAL may act as part of an incoherent feed-forward loop to control the establishment of a stable developmental program for the formation of flowers.

overall_design: Two microarray experiments performed in Arabidopsis lines expressing a LFY-GR construct. The first is a timecourse series identifying differential expresion following the induction of LFY expression. The other is a single timepoint identifying differential expression following LFY activation in the presence of protein synthesis inhibitors. All time points in both experiments have multiple replicates. Replicates are dye swapped.

first: Kevin

last: Goslin

first: Beibei

last: Zheng

first: Antonio

last: Serrano-MIslata

first: Liina

last: Rae

first: Patrick

first: Kamila

last: Kwasniewska

first: Bennett

last: Thomson

first: Diarmuid

middle: S

last: Ó'Maoiléidigh

first: Francisco

last: Madueño

first: Frank

last: Wellmer

first: Emmanuelle

last: Graciet


title: TLR signaling in C57BL/6J TLR7-tolerant CD3+ T-cells over B6 TLR7 null CD3+ T-cells.

city: Thessaloniki

first: Nikolaos

last: Zogas

address: Exokhi

institute: George Papanicolaou Hospital

summary: Murine CD3+ T-cells were immunomagnetically purified from the spleens of C57BL/6J mice and were pretreated in vitro for three days in the presence of R848 (5 μg/ml). Gene expression profile of wild type (WT) C57BL/6J TLR7-primed  T-cells, was compared to unmanipulated B6 TLR7 null CD3+ Τ-cells. We used Qiagen Toll-like Receptor RT2 Profiler PCR Array kit to quantitate gene expression profiling of the TLR signaling pathway.

first: Evangelia

last: Yannaki


title: 12plex_vitis_2011_02_48h-Défistim

status: Public on Apr 17 2017

first: Stéphanie

last: Pateyron

summary: 12plex_vitis_2011-02 - 12plex_vitis_2011_02_48h - Biological question (15 lines max): Identification of grape genes regulated in response to resistance inducer treatments. This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction. - The experiment took place in the greenhouse. Six week-herbaceous grape cutting (cv Marselan) were spray-treated with 5 resistance inducers, an adjuvant (used along with some inducers) and water as control. Plants were inoculated by Plasmopara viticola (downy midew) 24 h post-treatment. We used 5 plants per treatment. Leaf samples were harvested 24 h post-treatment and 48 h post-inoculation. Three biological repetitions were done. Each hybridization experiment was performed in comparison with water.

overall_design: 18 dye-swap - normal vs disease comparison

first: Stephanie

last: Huguet

first: Xavier

last: Daire

first: Sandrine

last: Balzergue

first: Marie-Laure


title: 12plex_vitis_2011_02_24h-Défistim

summary: 12plex_vitis_2011-02 - 12plex_vitis_2011_02_24h - Biological question (15 lines max): Identification of grape genes regulated in response to resistance inducer treatments. This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction. - Identification of grape genes regulated in response to resistance inducer treatments. This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction.

overall_design: 17 dye-swap - normal vs disease comparison,treated vs untreated comparison

last: Martin-Magniette


title: IL21R-expressing CD14+CD16+ monocytes expand in multiple myeloma patients leading to increased osteoclasts

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: Bone marrow monocytes are primarily committed to osteoclast formation. It is, however, unknown whether potential primary alterations are specifically present in bone marrow monocytes from patients with multiple myeloma, smoldering myeloma or monoclonal gammopathy of undetermined significance. We analyzed the immunophenotypic and transcriptional profiles of bone marrow CD14+ monocytes in a cohort of patients with different types of monoclonal gammopathies to identify alterations involved in myeloma-enhanced osteoclastogenesis. The number of bone marrow CD14+CD16+ cells was higher in patients with active myeloma than in those with smoldering myeloma or monoclonal gammopathy of undetermined significance. Interestingly, sorted bone marrow CD14+CD16+ cells from myeloma patients were more pro-osteoclastogenic than CD14+CD16-cells in cultures ex vivo Moreover, transcriptional analysis demonstrated that bone marrow CD14+ cells from patients with multiple myeloma (but neither monoclonal gammopathy of undetermined significance nor smoldering myeloma) significantly upregulated genes involved in osteoclast formation, including IL21RIL21R mRNA over-expression by bone marrow CD14+ cells was independent of the presence of interleukin-21. Consistently, interleukin-21 production by T cells as well as levels of interleukin-21 in the bone marrow were not significantly different among monoclonal gammopathies. Thereafter, we showed that IL21R over-expression in CD14+ cells increased osteoclast formation. Consistently, interleukin-21 receptor signaling inhibition by Janex 1 suppressed osteoclast differentiation from bone marrow CD14+ cells of myeloma patients. Our results indicate that bone marrow monocytes from multiple myeloma patients show distinct features compared to those from patients with indolent monoclonal gammopathies, supporting the role of IL21R over-expression by bone marrow CD14+ cells in enhanced osteoclast formation.

overall_design: To investigate the genes differentially expressed in monocytes of MGUS, SMM and MM patient, we performed gene expression profiling using Affymetrix GeneChip analysis of  monocytes purified from the bone marrow aspirates of MM, smoldering MM and MGUS patients.

first: Marina

last: Bolzoni

first: Domenica

last: Ronchetti

first: Paola

last: Storti

first: Gaetano

last: Donofrio

first: Valentina

last: Marchica

first: Sabrina

last: Bonomini

first: Andrea

last: Vecchi

first: Federica

last: Costa

first: Emanuela

last: Vicario

first: Daniela

last: Guasco

first: Denise

last: Toscani

first: Fabrizio

last: Accardi

first: Benedetta

middle: D

last: Palma

first: Carlo

last: Ferrari

first: Antonino

last: Neri

first: Franco

last: Aversa

first: Nicola

last: Giuliani


title: Plasma Circular RNAs, Hsa_circRNA_025016, Predicts Postoperative Atrial Fibrillation After Isolated Off-Pump Coronary Artery Bypass Grafting

status: Public on Apr 07 2017

city: shenyang

first: huishan

last: wang

state: liaoning

address: No.83, Wenhua Road

department: Department of Cardiovascular Surgery

institute: General Hospital of Shenyang Military Area Command

summary:
Rationale: Circular RNAs are pervasively expressed in highly diverged eukaryotes. Circular RNAs are more stable in body fluids, however, the link between circular RNA and onset of atrial fibrillation has never been investigated.

Objective: To identify plasma circular RNAs for diagnosing onset of atrial fibrillation after the cardiac surgery.

Methods and Results: Plasma circular RNAs expression was investigated in participants underwent isolated off-pump coronary artery bypass grafting. First, we used microarray to screen 15 circular RNAs in 30 plasma samples for diagnosing new onset of atrial fibrillation. Quantitative polymerase chain reaction assay was then applied to evaluate the expression of selected circular RNAs. Hsa_circRNA_025016 was upregulated in patients with onset of atrial fibrillation, with a high diagnostic accuracy by area under the receiver operating characteristic curve. The satisfactory diagnostic performance of hsa_circRNA_025016 persisted in validation cohort. Kyoto Encyclopedia of Genes and Genomes biological pathway analysis indicated that hsa_circ_025016 could participate in melanogenesis, insulin secretion, and thyroid hormone signaling pathway. There was a positive correlation between hsa_circ_025016 and fast blood glucose in both cohorts.

Conclusions: Hsa_circ_025016 is a novel biomarker of onset of atrial fibrillation after isolated off-pump coronary artery bypass grafting.

overall_design: Plasma Circular RNAs before surgery were collected. Plasma of patients with postoperative atrial fibrilltion and Patients without postoperative atrial fibrilltion were detected the expression of circular RNAs.

first: jian

last: zhang


title: SUCNR1-mediated chemotaxis of macrophages aggravates obesity-induced inflammation and diabetes.

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Obesity induces macrophages to drive inflammation in adipose tissue, a crucial step towards the development of type 2 diabetes. The tricarboxylic acid (TCA) cycle intermediate succinate is released from cells under metabolic stress and has recently emerged as a metabolic signal induced by proinflammatory stimuli. We therefore investigated whether succinate receptor 1 (SUCNR1) could play a role in the development of adipose tissue inflammation and type 2 diabetes. Succinate levels were determined in human plasma samples from individuals with type 2 diabetes and non-diabetic participants. Succinate release from adipose tissue explants was studied. Sucnr1 -/- and wild-type (WT) littermate mice were fed a high-fat diet (HFD) or low-fat diet (LFD) for 16 weeks. Serum metabolic variables, adipose tissue inflammation, macrophage migration and glucose tolerance were determined. We show that hypoxia and hyperglycaemia independently drive the release of succinate from mouse adipose tissue (17-fold and up to 18-fold, respectively) and that plasma levels of succinate were higher in participants with type 2 diabetes compared with non-diabetic individuals (+53%; p < 0.01). Sucnr1 -/- mice had significantly reduced numbers of macrophages (0.56 ± 0.07 vs 0.92 ± 0.15 F4/80 cells/adipocytes, p < 0.05) and crown-like structures (0.06 ± 0.02 vs 0.14 ± 0.02, CLS/adipocytes p < 0.01) in adipose tissue and significantly improved glucose tolerance (p < 0.001) compared with WT mice fed an HFD, despite similarly increased body weights. Consistently, macrophages from Sucnr1 -/- mice showed reduced chemotaxis towards medium collected from apoptotic and hypoxic adipocytes (-59%; p < 0.05). Our results reveal that activation of SUCNR1 in macrophages is important for both infiltration and inflammation of adipose tissue in obesity, and suggest that SUCNR1 is a promising therapeutic target in obesity-induced type 2 diabetes.

overall_design: Gene expression was profiled in white adipose tissue from wild-type and Sucnr1-knockout mice.

first: Janna

last: van Diepen

first: Rinke

last: Stienstra

first: Peter

last: Deen


title: Dietary zinc deficiency and supplementation in early life and mammary tumors development in adulthood female rats

status: Public on Apr 08 2017

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

country: Brazil

institute: Barretos Cancer Hospital

summary: Zinc deficiency during pregnancy and postnatal life can adversely affect the health and predispose to an increased risk of developing human diseases at adulthood.  The present study was designed to evaluate whether dietary zinc deficiency or supplementation during the pregnancy, lactation and juvenile stages interferes with the development of mammary tumors induced by 7,12-dimethylbenzanthracene (DMBA) in female Sprague-Dawley (SD) rats. Pregnant females SD were allocated into three groups: dams received diets containing adequate (35 mg/Kg chow), deficient (3 mg/Kg chow) or supplemented (180 mg/Kg chow) zinc levels during gestational day 10 (GD 10) until the litters weaning. Female offspring were allocated into three groups and received the same diets as their dams until postnatal day (PND) 51. At PND 51, females SD (n=16 each group) received a single dose of DMBA (50 mg/kg, ig) for initiation of mammary carcinogenesis, adequate zinc diets and were euthanized at PND 180. Tumors samples were collected and processed for histological evaluation and microarray analysis. Dietary zinc deficiency induced a significant reduction in female offspring body weight evolution at parturition, weaning and pubertal phases. At late in life, the early in life dietary zinc deficiency or supplementation did not alter the latency, incidence, multiplicity and volume or histological types of mammary tumors in relation to the adequate zinc group, and changed the expression of a small amount of genes. The present findings indicate that early-in life dietary zinc deficiency or supplementation did not significantly modify the susceptibility to development of mammary tumors induced by DMBA.

overall_design: Pregnant Sprague-Dawley (SD) rats (16 dams /group) were distributed into three groups: ZnA, dams fed adequate zinc diet (35 mg/Kg chow); ZnD, dams fed zinc deficient diet (3 mg/Kg chow); and ZnS, dams fed zinc supplemented diet (180 mg/Kg chow). These experimental diets were provided ad libitum to the dams from GD 10 until lactational day (LD) 21 (weaning). At PND 21, female offspring were allocated in their respective dietary intervention and received the same diet that dams intake during gestation and lactation phases until PND 51 (puberty). At PND 51, all animals received a single intragastric administration (i.g.) of DMBA (50 mg/kg, diluted in canole oil) and were fed adequate zinc diet until PND 180. At PND 180 the animals were euthanized for mammary tumor and gene expression analyses.

first: Flavia

middle: R

last: Silva

first: Tony

middle: F

last: Grassi

first: Joyce

last: Zapaterini

first: Luís

last: Barbisan


title: A transcriptional program for arbuscule degeneration during AM symbiosis is regulated by MYB1

first: Maria

middle: J.

last: Harrison

state: New York

address: 533 Tower Road

institute: Boyce Thompson Institute

summary:
The array experiment compares gene expression in roots of Medicago truncatula A17 and Medicago truncatula mutant mtpt4-1 colonized with Gigaspora gigantea.
This experiment enabled the identification of a plant transcriptional program associated with arbuscule degeneration. The experiment and data are described in Floss et al., Current Biology (in revision).

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: The experiment compares three independent biological replicate samples of A17 colonized with Gigaspora gigantea with three independent biological replicate samples of mtpt4-1 colonized with Gigaspora gigantea harvested 18 day post planting into inoculated substrate. This translates to approx. 11 days post contact with the spores. Colonized regions of the roots were identified based on the natural autofluorescence of Gigaspora gigantea and colonized regions were selected for RNA extraction.

first: S

last: Gomez


title: Circular RNA (circRNA) expression profiles in hypopharyngeal carcinoma tissues vs. adjacent normal mucosae detected by microarray

status: Public on Apr 06 2017

city: Jinan

first: shengda

last: cao

state: Shandong Province

address: wenhua west road

department: ENT

institute: Qilu hospital

overall_design: The expression profiles of circRNA in 4 pairs of hypopharyngeal carcinoma tissues and matched adjacent nomal mucosae were obtained through circRNA microarry detection.

first: Dapeng

last: Lei


title: Gene expression in rat striatum following carbon monoxide poisoning and hypoxic hypoxia

status: Public on Apr 03 2017

city: Tokyo

first: Shuichi

last: Hara

address: 6-1-1 Shinjuku, Shinjuku-ku

department: Forensic Medicine

institute: Tokyo Medical University

summary: We have proposed the existence of a threshold for brain damage, in terms of hydroxyl radical production in rat striatum, between poisoning of carbon monoxide (CO) at 1000 ppm and 3000 ppm, where blood CO-hemoglobin levels reach approximately 50% and over 70%, respectively. To search for factors involved in brain damage, we examined the effects of air, 1000 ppm CO, 3000 ppm CO and 5% O2 (hypoxic conditions comparable with those by 3000 ppm CO) on gene expression in rat striatum, using microarray analysis.

overall_design: Gene expression was measured in rat striatum which had been obtained at 0, 2, 6, or 12 hours after the 40-minute exposure to air, 1000 ppm CO, 3000 ppm CO or 5% O2 (a rat for each time of each exposure). The control is 0 hour after air.

first: Fumi

last: Kuriiwa

first: Masamune

last: Kobayashi

first: Hajime

last: Mizukami


title: Transcriptomic analysis to analyze gene expression of bacteria corroding iron

status: Public on Apr 04 2017

city: Bunkyo-ku

first: Tatsuya

last: Inoue

state: Tokyo

address: Yayoi 1-1-1

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

summary: To identify the mechanism of Microbial Influenced Corrosion (MIC) and the bacterial response toward corrosion, we conducted whole genome microarray expression profile. At log phase, the cell of Clostridium carboxidivorans using iron granule as an electron donor (corroding iron) was collected as a sample, and that of using syngas as an electron donor was collected as a control.

overall_design: Two sets of gene expression, which were C. carboxidivorans extracting  iron from iron granule and syngas was measeured.  Four independent experiments were performed  using different cultures.

last: INOUE

first: Shin-ichi

last: HIRANO


title: 68hctrl_68hcetrotide

city: Québec

first: Anne-Laure

last: Nivet

state: Québec

address: 2440 Hochelaga Blvd

country: Canada

institute: Laval University

summary: Transcriptional profiling of cows granulosa cells comparing granulosa cells from superstimulated control cows with granulosa cells from superstimulated cetrotide treated cows. Abstract:In cow, follicular growth stimulation (FSH) followed by a 44h-68h coasting (no FSH) period has been shown to be beneficial for developmental competence of aspirated oocytes. This process has been optimized but the associated physiology is not perfectly understood. During the above treatment LH pulse frequency is basal as the animal are in the luteal phase. The goal of this study was to test the existence of a beneficial effect of basal LH pulses during competence acquisition. To answer to this question, LH pulses have been pharmacologically inhibited during the optimal coasting period with GnRH antagonists. Commercial milking cycling cows (n=5) were stimulated with 3 days of FSH followed by a coasting period of 68H, with and without cetrorelix injections. At the scheduled time, transvaginal aspirations of immature oocytes were performed, followed by IVF while follicular cells were pooled for each animal and were snap-frozen. Granulosa cells RNA was extracted amplified and hybridized on Embryogene bovine microarray slides. Data were normalized with Loess, and analyzed with Limma procedure. Follicle size group proportions and granulosa cell transcriptome were studied. (1) There was a significant reduction in >10mm diameter follicles with cetrorelix comparing to without treatment. (2) Transcriptome analysis reveals 724 tanscripts potentially regulated by basal gonadotropins before LH surge. Among this LH influenced gene group, 84 transcripts were positively associated to developmental competence. This work allows the identification of subpopulations of gene signals dependant from LH or not, and permits a better comprehension of the implication of basal LH in follicle growth and in competence acquisition process.

overall_design:
Two-condition experiment, control vs cetrotide treated cows. Biological replicates: 3 control cows, 3 cetrotide treated cows. Dye swap experiments, two colors, one replicate per array.

Please note that the 'characteristics: Time' values represent the duration between the last FSH injection and the ovum pick up.

first: Anne-laure

first: Christian

last: Vigneault

first: Patrick

last: Blondin

first: Marc-André

last: Sirard


title: IMPACT OF MALE FERTILITY STATUS ON THE TRANSCRIPTOME OF THE BOVINE EPIDIDYMIS

status: Public on Mar 31 2017

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

summary: Study question: Can region-specific transcriptional profiling of the epididymis from fertile and sub-fertile bulls predict the aetiology of fertility/subfertility in males?  Summary answer:The highly regulated gene expression along the bovine epididymis is affected by the fertility status of bulls used for artificial insemination. What is known already: In mammals, sperm maturation and storage occur in the epididymis. Each epididymal segment has his own transcriptomic signature that modulates the intraluminal composition that governs sequential modifications of the maturing male gamete. Main results and the role of chance: Hierarchical clustering and Principal Component Analysis revealed a clear separation between caput, corpus and cauda epididymides. Some transcripts characterize a particular anatomical segment, whereas others are expressed in two out of three epididymal segments. GO analysis allowed deduction of specific functions played by each epididymal segment. The transcriptional profiles between fertile vs. sub-fertile conditions clustered most closely in the corpus and cauda segments, whereas the profiles in the caput segment were distinct between fertile and sub-fertile bulls. Of the differently expressed genes, ten (including AKAP4, SMCP, SPATA3, TCP11, ODF1, CTCFL, SPATA18, ADAM28, SORD and FAM161A) were found to exert functions related to reproductive systems and 5 genes (including DEAD, CYST11, DEFB119, DEFB124 and MX1) were found to be associated with the defence response. Limitations, reasons for caution: Further work is required to correlate these modulations of epididymal functions with sperm fertilizing ability in order to understand the aetiology of certain cases of idiopathic infertility in livestock and men. Wider implications of the findings: As fertility can be quantified in bulls used for artificial insemination, this species is a unique model to aid in the understanding of male fertility/subfertility in man.Our data provide a molecular characterization that will facilitate advances in understanding the involvement of epididymalphysiology in sub/infertility aetiology.

overall_design: Epididymides from 6 Holstein bulls with documented fertility were used. These bulls were divided into 2 groups: high fertility (HF) (n = 3), and medium–low fertility (n = 3) and their epididymal transcriptomic profiles were analyzed. Bovine cDNA microarray probing and bioinformatic tools were used to identify differentially expressed genes between caput, corpus and cauda epididymidal tissues of bulls with documented fertility index.

first: Christine

last: Légaré

first: Ayodélé

last: Akintayo

first: Robert

last: Sullivan


title: ChIP-chip analysis of RNAP and Sigma factor binding to the Salmonella enterica serovar Typhimurium chromosome

status: Public on Apr 01 2017

first: Shane

last: Dillon

address: Kevin Street

department: School of Biological Sciences

institute: Dublin Institute of Technology

type: Genome binding/occupancy profiling by array

summary: ChIP-chip analysis of RNA Polymerase (RNAP), RpoD, RpoE, RpoH and RpoN in exponential phase (OD 0.2) and early stationary phase (OD 2.0) Salmonella enterica serovar Typhimurium SL1344 cultures

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Analysis of RNA Polymerase and Sigma factor binding in Salmonella Typhimurium SL1344 cultures grown in Lennox Broth (LB).

first: Andrew

last: Cameron

first: Carsten

last: Krӧger

first: Laurens

last: Beran

first: Charles

middle: J

last: Dorman


title: Differential gene expression analysis of bovine macrophage cells following exposure to Penicillium mycotoxins

city: Guelph

first: Se-Young

last: Oh

state: Ontario

address: 50 Stone Rd East

department: Animal Bioscience

institute: University of Guelph

summary:
Mycotoxins produced by fungal species commonly contaminate livestock feedstuffs. Citrinin (CIT) and ochratoxin A (OTA) are mycotoxins produced by Penicillium spp. and commonly co-occur. Both CIT and OTA can modulate the immune response by inhibiting cell proliferation and differentiation, changing in cell metabolism, or triggering programmed cell death.
In this study, we used microarrays to determine the effects of CIT, OTA or both on the bovine macrophage (BoMac) transcriptome.

overall_design: BoMacs (1.0 x 106 per treatments) were in vitroly exposed to sublethal concentrations (IC25 to provide the similar stress level to the cells without causing overt cytoxicity) of CIT, OTA or both combined for 6 and 24 hours. tRNA was extracted and hybridized on Affymetrix microarrays. The trials were repeated three times independently to ensure the reproducibility of the study.

first: Kristen

last: Brennan

first: Daniel

middle: E

last: Graugnard


title: The SAGA complex in the rice pathogen Fusarium fujikuroi: structure and functional characterization

city: Neuherberg, Germany

last: Sieber

address: Ingolstädter Landstraße 1

department: Institute of Bioinformatics and Systems Biology

institute: Helmholtz Zentrum München

summary:
Post-translational modification of histones is a crucial mode of transcriptional regulation in eukaryotes. A well-described acetylation modifier of certain lysine residues is the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex assembled around the histone acetyltransferase Gcn5 in Saccharomyces cerevisiae. We identified and characterized the SAGA complex in the rice pathogen Fusarium fujikuroi, well-known for producing a large variety of secondary metabolites (SMs). By using a co-immunoprecipitation approach, almost all of the S. cerevisiae SAGA complex components have been identified, except for the ubiquitinating DUBm module and the chromodomain containing Chd1. Deletion of GCN5 led to impaired growth, loss of conidiation and alteration of SM biosynthesis. Furthermore, we show that in F. fujikuroi Gcn5 is essential for the acetylation of several histone 3 lysines, i.e. H3K4, H3K9, H3K18 and H3K27. A genome-wide microarray analysis revealed differential expression of about 30% of the genome with an enrichment of genes involved in primary and secondary metabolism, transport and histone modification. HPLC-based analysis of known SMs revealed significant alterations in the Δgcn5 mutant. While most SM genes were activated by Gcn5 activity, the biosynthesis of the pigment bikaverin was strongly increased upon GCN5 deletion underlining the diverse roles of the SAGA complex in F. fujikuroi.
Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289 and the Δgcn5 mutant under nitrogen starvation and nitrogen sufficient conditions.

overall_design: In this study we hybridized in total 12 microarrays using total RNA recovered from a wild-type culture of F. fujikuroi IMI58289 and Δgcn5 mutant culture. All cultures were grown in a 6 mM Gln (10%) and a 60 mM Gln ICI liquid medium (100%). For each combination of culture and medium in total three biological replicate were created. Each chip measures the expression level of 14,808 genes from F. fujikuroi IMI58289 with eight 60-mer probes.

first: Sarah

last: Rösler

first: Katharina

last: Kramer

first: Iris

last: Finkemeier

first: Hans-Ulrich

last: Humpf

first: Bettina

last: Tudzynski


title: Illumina SNP array data for acute myeloid leukemia samples

status: Public on Apr 10 2017

city: Philadelphia, PA

first: Richard

last: Aplenc

state: PA

address: 3501 Civic Center Blvd

department: Division of Oncology

institute: Children's Hospital of Philadelphia

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

summary:
Pediatric patients with de novo acute myeloid leukemia. To define genomic architecture, we performed genome-wide copy number abberation analysis in 460 paired diagnostic-remission bone marrow aspirates.
Illumina SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic and remission bone marrow samples.

overall_design:
Copy number abberation analysis of Affymetrix 6.0 SNP arrays (254 sample pairs) and Illumina 2.5M Omni arrays (206 sample pairs) was performed for 460 acute myeloid leukemia samples
This Series represents the Illumina dataset.

first: Soheil

last: Meshinchi

first: Marijana

last: Vujkovic

first: Rhonda

last: Ries


title: Shoot-to-root mobile polypeptides involved in systemic regulation of nitrogen acquisition

city: Nagoya

first: Yoshikatsu

last: Matsubayashi

state: Aichi

address: Chikusa

department: Graduate School of Science

institute: Nagoya University

summary:
Plants uptake nitrogen (N) from the soil mainly in the form of nitrate. However, nitrate is often distributed heterogeneously in natural soil. Plants, therefore, have a systemic long-distance signaling mechanism by which N-starvation on one side of the root leads to a compensatory N uptake on the other N-rich side. This systemic N acquisition response is triggered by a root-to-shoot mobile peptide hormone, C-terminally Encoded Peptide (CEP), originating from the N-starved roots, but the molecular nature of the descending shoot-to-root signal remains elusive. Here, we show that phloem-specific polypeptides that are induced in leaves upon perception of root-derived CEP act as descending long-distance mobile signals translocated to each root. These shoot-derived polypeptides, which we named CEP Downstream 1 (CEPD1) and CEPD2, upregulate the expression of the nitrate transporter gene NRT2.1 in roots specifically when nitrate is present in the rhizosphere. Arabidopsis plants deficient in this pathway show impaired systemic N-acquisition response accompanied with N-deficiency symptoms. These fundamental mechanistic insights should provide a conceptual framework for understanding systemic nutrient acquisition responses in plants.
We prepared total RNA from vascular tissues of wild type, CEP1-treated wild type, and cepr1-1 mutant, and used a microarray analysis to identify genes specifically induced by CEP1.

overall_design: Total RNA isolated from the vascular tissues derived from 200 cotyledons of wild type, wild type grown in the presence of 1 uM CEP1 and cepr1-1 mutant were subjected to microarray analysis. Labeled complementary RNA was hybridized with an Affymetrix Genechip Arabidopsis Gene 1.0 ST array.

first: Yuri

last: Ohkubo

first: Mina

last: Tanaka

first: Ryo

last: Tabata

first: Mari

last: Ogawa-Ohnishi


title: Utilization of a Genomic Classifier for Prediction of Metastasis Following Salvage Radiation Therapy after Radical Prostatectomy

city: Vancouver

first: Elai

last: Davicioni

state: British Columbia

address: 1038 Homer st

institute: GenomeDx Biosciences Inc

summary: To test whether a genomic classifier (GC) predicts development of metastatic disease in patients treated with salvage radiation therapy (SRT) after radical prostatectomy (RP).

overall_design: 70 primary prostate cancer tumor (radical prostatectomy, FFPE) specimens from patients at the Durham VA who recieved post-RP radiation therapy.

first: Stephen

last: Freedland

first: Voleak

last: Choeurng

first: Lauren

last: Howard

first: Amanda

last: De Hoedt

first: Marguerite

last: du Plessis

first: Kasra

last: Yousefi

first: Lucia

middle: L

last: Lam

first: Christine

last: Buerki

first: Seong

last: Ra

first: Bruce

last: Robbins

first: Edouard

last: Trabulsi

first: Nikhil

last: Shah

first: Firas

last: Abdollah

first: Felix

middle: Y

last: Feng

first: Adam

middle: P

last: Dicker

first: Robert

last: Karnes

last: Den


title: Host responses that correlate with respiratory droplet transmission of swine-origin influenza viruses in ferrets.

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: The determinants of influenza transmission remain poorly understood. Swine influenza viruses preferentially attach to receptors found in the upper airways; however, most swine influenza viruses fail to transmit efficiently from swine to humans, and from human-to-human. The pandemic 2009 H1N1 (H1N1pdm) virus was a rare exception of a swine virus that acquired efficient transmissibility from human-to-human, and is reflected in efficient respiratory droplet transmission in ferrets. We hypothesize that virus-induced host responses in the upper airways correlate with airborne transmission in ferrets. To address this question, we used the H1N1pdm virus and swine influenza A/swine/Hong Kong/201/2010 (HK201) virus that has comparable titre in the ferret nasopharynx, but it exhibits differential transmissibility in ferrets via respiratory droplet route. We performed a transcriptomic analysis of tissues from the upper and lower respiratory tract from ferrets infected with either H1N1pdm or HK201 viruses using ferret-specific Agilent oligonucleotide arrays. We found differences in the kinetics of the innate immune response elicited by these two viruses that varied across tissues.

overall_design: Ferrets were mock inoculated with 0.5mL media or inoculated with 105 TCID50 of the A/CA/04/09 (H1N1) or A/Sw/HK/ 210/10 (H1N1) influenza viruses intra-nasally. There are a total of 9 ferrets per virus group and six ferrets for the mock group. Ferrets were euthanized at day 1 (n = 4 per virus group) and day 2 (n = 5 per virus group) post-inoculation (p.i.). Three mock inoculated ferrets were euthanized at days 1 and 2 p.i. Tissues from nasal turbinate, soft palate, pharynx, trachea, bronchus, and lungs were collected at necropsy, placed in RNAlater overnight at 4°C and conserved at -80°C.  RNA was extracted and gene expression was analyzed by custom 4x180K ferret-specific oligonucleotide arrays (Agilent Cat# G4862A, design ID 48472)

first: Jennifer

last: Tisoncik-Go

first: Dariusz

last: Przybylski

first: Jean

last: Chang

first: Andrew

last: Nishida

first: Aviv

last: Regev

first: Malik

last: Peiris

first: Hui-Ling

last: Yen


title: 12plex_pea_2013_02_g      -Water stress and seed filling in pea

status: Public on Apr 05 2017

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: 12plex_pea_2013_02 - 12plex_pea_2013_02_g       - What is the effect of a moderate water stress on seed filling (reserve accumulation) and nitrogen remobilisation in pea (Pisum sativum)         - Pea plants (genotype Cameor) were subjected to a moderate water stress at the beggining of the seed filling period (12 Days After Pollination) of the second flowering node for a period of 8 days. Samples were collected from Well Watered (WW) plants at the beginning of the stress imposition (point A, T=0), and from Water-Stressed (WS) and WW control plants at the end of the drought period (point B, T=+8). Samples named SEED consisted of seeds from the pod of the second flowering node (seed-WW-A, seed-WW-B and Seed-WS-B). Samples named LEAF consisted of the leaves and stem sections from the two vegetative nodes below the first flowering node (leaf-WW-A, Leaf-WW-B and Leaf-WS-B). Each sample consited of a pool of 3 individual plants and 4 repetitions per condition were carried out.

overall_design: 12 dye-swap - treated vs untreated comparison

first: Dao-xiu

last: Zhou

first: Vanessa

last: Vernoud

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Compartment-specific investigation of differential gene expression profiles in lungs with idiopathic pulmonariy fibrosis (IPF)

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Lung tissues were collected from patients with IPF undergoing lung transplantation. Non-transplanted donor lung tissue showing no evidence of interstitial lung disease served as healthy controls. Septa from different regions of the lungs were mircodissected and their RNA was subjected to microarray-analysis. RNA from 10 heathy donor tissues was pooled and used as a pooled reference. From each of the 10 IPF patients, samples were collected once from “healthy looking” (non-fibrotic) regions and from fibrotic loci.

overall_design: Two-color design, 3 groups: one pooled healthy control sample (from n=10 patients), 10 samples from septa from normal and from fibrotic of n=10 patients.

first: Ludger

last: Fink

first: Günther

last: Andreas


title: Diurnal variation for rice leaves in Furukawa field in 2014

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Furukawa.
Time-course transcriptional profiling of rice leaf in Furukawa field in 2014. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Furukawa in Japan. Leaf samples were harvested in a 2 hr-interval for 13 times. This set corresponds to one-day time-series data. Transplanting dates and sampling dates varied as reported in each sample record.


title: Diurnal variation for rice leaves in Toyama field in 2014

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Toyama.
Time-course transcriptional profiling of rice leaf in Toyama field in 2014. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Toyama in Japan. Leaf samples were harvested in a 2 hr-interval for 13 times. This set corresponds to one-day time-series data. Transplanting dates and sampling dates varied as reported in each sample record.


title: Diurnal variation for rice leaves in Sapporo field in 2014

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Sapporo.
Time-course transcriptional profiling of rice leaf in Sapporo field in 2014. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Sapporo in Japan. Leaf samples were harvested in a 2 hr-interval for 13 times. This set corresponds to one-day time-series data. Transplanting dates and sampling dates varied as reported in each sample record.


title: Response to SARS-CoV in the PreCC

city: Chapel Hill

first: Martin

last: Ferris

state: NORTH CAROLINA

address: CB 7292, Genetics

institute: University of North Carolina- Chapel Hill

summary: In order to narrow candidate QTL loci into relevant genes driving disease differences, we assessed transcriptional differences across the pre-CC population used to map phenotypic QTL.  We integrate this normalized expression data with polymorphisms underneath a candidate locus to arrive at a high priority candidate gene which had genetic variants private to the causal haplotype and also had expression strongly correlated with the appropriate trait (SARS-CoV viral lung load at 4 DPI).

overall_design: 68 samples each derived from a different CC line with expression measured from lung tissue at day 4 post infection. Infection was with the mouse adapted SARS-Coronavirus MA15 strain

first: M

first: D

last: Bottomly

first: S

middle: K

last: McWeeney


title: Effect of lipopolysachharide (LPS) on the acute expression of inflammatory mRNAs and microRNAs in the mouse oviduct

status: Public on Apr 14 2017

city: Lexington

first: Phillip

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

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

overall_design: Refer to individual Series


title: Diurnal variation for rice leaves in Tsukuba field in 2014

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Tsukuba.
Time-course transcriptional profiling of rice leaf in Tsukuba field in 2014. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Tsukuba in Japan. Leaf samples were harvested in a 6 hr(or 8hr)-interval for 13 times. This set corresponds to three-day time-series data. Transplanting dates varied as reported in each sample record.


title: Expression data from Saccharomyces cerevisiae BY4741 and BY4741hsp30Δ cells grown at 30°C and following exposure at 40°C for 30 min.

status: Public on Apr 20 2017

city: Delhi

first: Amitabha

last: Chakrabarti

state: Delhi

address: Lucknow Road

department: Molecular Biology

country: India

institute: Defence Institute of Physiology and Allied Sciences

summary:
The Target Of Rapamycin (TOR) pathway is down-regulated in hsp30Δ cells.
We compared the gene expression program of hsp30Δ cells with that of its wild type counterpart (BY4741) to identify activities associated with Hsp30.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Total RNA was isolated using the Qiagen RNeasy Mini kit from Log phase BY4741 and hsp30Δ::kanMX cells grown in YPD medium at 30°C and following exposure at 40°C for 30 min and sent to Ocimum Biosolutions India, to identify genes that were either up-regulated or down-regulated in hsp30Δ cells as compared to the control.

first: Ramesh

middle: C

last: Meena


summary: au15-05_fit - differential gene expression in a.tha. depending on mutation in fit - Transcriptomical changes in transgenic plants that carry a point mutation in FIT. - Differential gene expression in A. thaliana seedlings depending on the introduction of a point mutation in FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) under iron deficient conditions.

overall_design: 18 dye-swap - gene knock out,genotype comparaison,normal vs transgenic comparaison

first: Petra

last: Bauer


title: Diurnal variation for rice leaves in Takatsuki field in 2014

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Takatsuki.
Time-course transcriptional profiling of rice leaf in Takatsuki field in 2014. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Takatsuki in Japan. Leaf samples were harvested in a 2 hr-interval for 13 times. This set corresponds to one-day time-series data. Transplanting dates and sampling dates varied as reported in each sample record.


title: Diurnal variation for rice leaves in Fukuyama field in 2014

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Fukuyama.
Time-course transcriptional profiling of rice leaf in Fukuyama field in 2014. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Fukuyama in Japan. Leaf samples were harvested in a 2 hr-interval for 13 times. This set corresponds to one-day time-series data. Transplanting dates and sampling dates varied as reported in each sample record.


title: Diurnal variation for rice leaves in Fukuoka field in 2014

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Fukuoka.
Time-course transcriptional profiling of rice leaf in Fukuoka field in 2014. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Fukuoka in Japan. Leaf samples were harvested in a 2 hr-interval for 13 times. This set corresponds to one-day time-series data. Transplanting dates and sampling dates varied as reported in each sample record.


title: Impact of exposure to environmentally-relevant concentrations of ionic silver and nanosilver on thyroid hormone-dependent postembryonic development of the North American bullfrog (Rana catesbeiana)

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

institute: University of Victoria

summary: Nanoparticles (<100 nm) are engineered to have unique physico-chemical properties compared to their larger counterparts. Nanosilver (nAg) is the most prevalent nanoparticle in consumer products due to its strong antimicrobial action. While nAg toxicity at high concentrations has been well described, the potential for sublethal effects at or below regulatory guidelines is relatively unknown. Amphibian metamorphosis is mediated by thyroid hormone (TH) and can be precociously induced by the addition of exogenous hormone. Low concentrations of nAg have been shown to disrupt TH-dependent responses in cultured premetamorphic Rana catesbeiana tadpole tail fin. The present study examined the effects of exposure to an environmentally relevant concentration (6 µg/L) of either nAg or ionic silver (iAg) on premetamorphic tadpoles in the absence and presence of exogenous TH. Disruption of thyroid hormone-mediated signalling in brain and liver transcriptomes was evaluated using the MAGEX cDNA microarray.

platform_organism:
Xenopus laevis
Aquarana catesbeiana
Lithobates pipiens

overall_design: Six premetamorphic tadpoles were randomly selected from each treatment condition (n=12) and the status of brain and liver transcriptomes determined by MAGEX cDNA array analysis.

first: Caren

last: Helbing


title: Diurnal variation for rice leaves in Tsukuba field in 2013

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Tsukuba.
Time-course transcriptional profiling of rice leaf in Tsukuba field in 2013. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
4 day time-series with 6h (or 8h) interval were sampled for 4 developmental stages with no replicate.
The submitted samples were field transcirptome data in a paddy field at Tsukuba in Japan. Leaf samples were harvested in a 6 hr(or 8hr)-interval for 13 times. This set corresponds to three-day time-series data. Transplanting dates varied as reported in each sample record.


title: Anti-CD3-induced activation of intestinal intraepithelial lymphocytes (IEL)

city: London

first: Lucie

last: Abeler-Dörner

address: Great Maze Pond

department: Immunobiology

country: United Kingdom

institute: King's College London

summary: The experiment was designed to assess whether conventional and unconventional IEL differ in their response to activation.

overall_design: Total RNA from activated TCRαβ CD8αβ and TCRγδ CD8αα IEL stimulated with anti-CD3 for 24 hours compaired to unactivated samples

first: Anna

last: Bas Forsberg

first: Robert

last: Andrews

first: Adrian

last: Hayday


title: Profiling transcriptomes of human SH-SY5Y neuroblastoma cells exposed to maleic acid

status: Public on Mar 14 2017

city: Kaohsiung

first: Chun-Wei

last: Tung

address: No. 100, Shih-Chuan 1st Rd.

country: Taiwan

institute: Kaohsiung Medical University

summary: A microarray-based transcriptome profiling was performed to provide a better understanding of  the effects of maleic acid on human. Gene expression profiles of human neuroblastoma SH-SY5Y cells exposed to three concentrations of maleic acid (10, 50 and 100 μM) for 24 h were analyzed.

overall_design: To get better insights into the effects of maleic acid on neuronal cells, the gene expression profiles of SH-SY5Y cells treated with three doses (10, 50 and 100 μM) of maleic acid along with control cells were examined.

first: Chia-Chi

last: Wang


title: Diurnal variation for rice leaves in Takatsuki field in 2013

first: Takeshi

summary:
Time-course transcriptional profiling of rice leaf in Takatsuki field in 2013. This experiment was performed to analyze the dynamics of field transcriptome data.
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Takatsuki.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Takatsuki in Japan. Leaf samples were harvested in a 2 hr-interval for 13 times. This set corresponds to one-day time-series data. Transplanting dates and sampling dates varied as reported in each sample record..


title: Diurnal variation for rice leaves in Sapporo field in 2013

summary:
Time-course transcriptional profiling of rice leaf in Sapporo field in 2013. This experiment was performed to analyze the dynamics of field transcriptome data.
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan.
In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Sapporo.

overall_design:
24h time series with 2h interval were sampled for 1 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Sapporo in Japan. Leaf samples were harbested in a 2 hr-interval for 13 times. This set corresponds to one-day time-series data. Transplanting dates and sampling dates varied as reported in each sample record..


title: Differentiation of human and murine induced pluripotent stem cells to microglia-like cells [mouse]

status: Public on Mar 02 2017

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Microglia are the resident inflammatory cells of the central nervous system (CNS) and have important roles in development, homeostasis and a variety of neurologic and psychiatric diseases.  Difficulties in procuring human microglia have limited their study and hampered the clinical translation of microglia-based treatments shown to be effective in animal disease models.  Here, we report the differentiation of human induced pluripotent stem cells (iPSC) into microglia-like cells by exposure to defined factors and co-culture with astrocytes.  These iPSC-derived microglia (iPS-MG) have the phenotype, gene expression profile and functional properties of brain-isolated microglia.  Murine iPS-MG generated using a similar protocol have equivalent efficacy to primary brain-isolated microglia in the treatment of murine syngeneic intracranial malignant gliomas.   The ability to generate human microglia facilitates the further study of this important CNS cell type and raises the possibility of their use in personalized medicine applications.

overall_design: 24 Mouse samples: 3 iPSC (induced pluripotent stem cell), 3 iPS-MG (GFP+ iPSC-derived microglia), 3 neo-MG (neonatal microglia), 3 ad-MG (adult microglia), 3 DC (dendritic cell), 3 NSC (neural stem cell), 3 bm-Mac (bone marrow macrophage), 3 p-Mac (peritoneal macrophage).

first: Hetal

last: Pandya

first: Michael

last: Shen

first: David

middle: M

last: Ichikawa

first: Andrea

last: Sedlock

first: Yong

last: Choi

first: Gloria

last: Kim

first: Mason

last: Brown

first: Abdel

last: Elkhaloun

first: Dragan

last: Maric

first: Dorian

last: McGavern

first: Harry

last: Malech

first: John

last: Park


title: Arabidopsis Col0 5 week-old plants: control vs 25 minutes of exposure to mild heat stress 27 degrees Celsius

status: Public on Mar 01 2017

city: Colchester

first: Ruben

last: Alvarez-Fernandez

address: Wivenhoe Park

department: Biological Sciences

institute: University of Essex

summary: Transcriptional profiling of fully developed leaves of Arabidopsis Col0 plants heat-stressed for 25 min at 27.7 degrees Celsius. Goal was to isolate and study the influence of temperature and vpd change in the 30 min high light-stress experiments, since the Isolight rises leaf temperature to 27.5C and increases the vpd from 5 min of exposure.

overall_design: two-condition, two-colour experiment, Control vs. heat stress, 4 biological replicates per treatment. The experiment comprised a single 4x44 Agilent V4 microarray slide with a dye-swap.

first: Phillip

last: Mullineaux


title: Arabidopsis Col0 5 week-old plants: control vs 30 minutes of exposure to high light stress (1000 umol m-2 s-1)

summary: Transcriptional profiling of fully developed leaves of Arabidopsis Col0 after 30 min of high-light stress (1000 umol*m-2*s-1). Goal was to find early transcriptional responses to immediate high-light stress, before acclimation responses appear.

overall_design: two-condition, two-colour experiment, Control vs. light stress, 4 biological replicates per treatment. The experiment comprised a single 4x44 Agilent V4 microarray slide with a dye-swap.


title: Diurnal variation for rice leaves in Toyama field in 2012

last: Izawa

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan.
In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Toyama.

overall_design:
Time-course transcriptional profiling of rice leaf in Toyama field in 2012. This experiment was performed to analyze the dynamics of field transcriptome data.
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.


title: Diurnal variation for rice leaves in Fukuyama field in 2013

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan.
In this seires of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Fukuyama.
Time-course transcriptional profiling of rice leaf in Fukuyama field in 2013. This experiment was performed to analyze the dynamics of field transcriptome data.


title: Diurnal variation for rice leaves in Furukawa field in 2013

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan.
In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Furukawa.
Time-course transcriptional profiling of rice leaf in Furukawa field in 2013. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Furukawa in Japan. Leaf samples were harvested in a 2 hr-interval for 13 times. This set corresponds to one-day time-series data. Transplanting dates and sampling dates varied as reported in the data sheet.


title: Diurnal variation for rice leaves in Toyama field in 2013

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Toyama.
Time-course transcriptional profiling of rice leaf in Toyama field in 2013. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Toyama?in Japan. Leaf samples were harvested in a 2 hr-interval for 13 times. This set corresponds to one-day time-series data. Transplanting dates and sampling dates varied as reported in each sample record.


title: Genes expression analysis of 3B7N regulation of hypooctyl elongation under continuous blue light irradiation

status: Public on Feb 28 2017

city: Yokohama

first: Wen Dee

last: Ong

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: Biomass Engineering

institute: RIKEN

summary: To understand the transcript regulation of early Arabidopsis seedlings developments with 3B7N under continuous blue light irradiation.

overall_design: Genes expression profiles of 3B7N treatment on WT and cry1cry2 were evaluated.  3B7N effect was evaluated by comparing 3B7N-treated sample to respective genotype sample with DMSO treatment.

first: Wen-Dee


title: Genes expression analysis of chemical-induced hypooctyl elongation under blue light irradiation

summary: To understand the transcript regulation of early Arabidopsis seedlings developments with different chemicals under continuous blue light irradiation.

overall_design: Three chemicals which induced different hypocotyl growth length in WT Arabidopsis seedlings were evaluated with three replicates conducted for each chemical. The profile for each chemical was analyzed againts sample with DMSO treatment as control.


title: Chemical-induced inhibition of blue light-mediated seedling development in Arabidopsis

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

overall_design: Refer to individual Series


title: Diurnal variation for rice leaves in Fukuoka field in 2013

first: Takeshi

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan.
In this seires of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Fukuyama."
Time-course transcriptional profiling of rice leaf in Fukuoka field in 2013. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
24h time series with 2h interval were sampled for 2 developmental stage with no replicate.
The submitted samples were field transcirptome data in a paddy field at Fukuyama in Japan. Leaf samples were harbested in a 2 hr-interval for 13 times. This set corresponds to one-day time-seires data. Transplanting dates and sampling dates varied as reported in each sample record.


title: Transcriptome response of the Streptococcus pneumoniae D39 wild-type to Naicin

status: Public on Feb 24 2017

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Transcriptome Comparison of the Streptococcus pneumoniae D39 wild-type grown in CDM with 0 mM to 10mM Niacin

overall_design: Two conditions design comparison of one strain including a dye swap.

first: Muhammad

last: Afzal

first: Oscar

last: Kuipers


title: Two time-points for fertilized rice leaves in Tsukuba field in 2013

summary:
We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this seires of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Tsukuba.
Time-course transcriptional profiling of rice leaf of fertilization in Tsukuba field in 2013. This experiment was performed to analyze the dynamics of field transcriptome data.

overall_design:
The submitted samples were field transcirptome data in a paddy field at Tsukuba in Japan. Leaf samples were harvested in a 6 hr(or 8hr)-interval for 13 times. This set corresponds to three-day time-seires data. Transplanting dates varied as reported in each sample record. The fertilizated rice leaves were collected at 10:40 and 16:40 with no replicate.
Fertilizated rice leaves were collected at 10:40 and 16:40 with no replicate.