title: Identification of glaikit in a genome-wide expression profiling for axonal bifurcation of the mushroom body in Drosophila (29 C)

status: Public on Apr 11 2017

city: Asahimachidori, Chuo-ku, Niigata-shi

first: Yohei

last: Nitta

state: Niigata

address: 757, Ichibancho,

institute: Niigata University

summary: Axonal branching is a fundamental requirement for sending electrical signals to multiple targets. However, despite the importance of axonal branching in neural development and function, the molecular mechanisms that control branch formation are poorly understood. Previous studies have hardly addressed the intracellular signaling cascade of axonal bifurcation characterized by growth cone splitting. Recently we reported that DISCO interacting protein 2 (DIP2) regulates bifurcation of mushroom body axons in Drosophila melanogaster. DIP2 mutant displays ectopic bifurcations in α/β neurons. Taking advantage of this phenomenon, we tried to identify genes involved in branching formation by comparing the transcriptome of wild type with that of DIP2 RNAi flies. After the microarray analysis, Glaikit (Gkt), a member of the phospholipase D superfamily, was identified as a downstream target of DIP2 by RNAi against gkt and qRT-PCR experiment. Single cell MARCM analysis of gkt mutant phenocopied the ectopic axonal branches observed in DIP2 mutant. Furthermore, a genetic analysis between gkt and DIP2 revealed that gkt potentially acts in parallel with DIP2. In conclusion, we identified a novel gene underlying the axonal bifurcation process.

overall_design: The central brain was isolated at 24 hrs APF to compare the entire gene expression profiles of OK107-Gal4/ UAS-dicer2;; UAS-DIP2-RNAi (DIP2 RNAi) with those of OK107-Gal4/ UAS-dicer2 (control). The experiments were performed in two biological replicates.


title: Identification of glaikit in a genome-wide expression profiling for axonal bifurcation of the mushroom body in Drosophila (25 C)

country: Japan

overall_design: The central brain was isolated at 24 hrs APF to compare the entire gene expression profiles of OK107-Gal4/ UAS-dicer2;; UAS-DIP2-RNAi (DIP2 RNAi) with those of OK107-Gal4/ UAS-dicer2 (control). The experiments were performed in three biological replicates.


title: Identification of glaikit in a genome-wide expression profiling for axonal bifurcation of the mushroom body in Drosophila (white pupa)

overall_design: The central brain was isolated at white pupal stage to compare the entire gene expression profiles of OK107-Gal4/ UAS-dicer2;; UAS-DIP2-RNAi (DIP2 RNAi) with those of OK107-Gal4/ UAS-dicer2 (control). The experiments were performed in three biological replicates.


title: Identification of glaikit in a genome-wide expression profiling for axonal bifurcation of the mushroom body in Drosophila

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

overall_design: Refer to individual Series


title: Bioenergetics status determines motor neuron vulnerability in spinal muscular atrophy

status: Public on Apr 10 2017

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

summary: Comparative gene expression profiling of motor neurons innervating the extensor digitorum longus (disease-resistant), gastrocnemius (intermediate vulnerability), and tibialis anterior (vulnerable) muscles in mice to determine the factors underlying their selective vulnerability in sinal muscular atrophy.

overall_design: Gene expression profiling utilised total RNA extracted from motor neurons derived from normal mice on an SMA background to investigate selective vulnerability of motor neurons

first: Penelope

last: Boyd

first: Wen-Yo

last: Tu

first: Rachael

middle: A

last: Powis

first: Hannah

last: Shorrock

first: Sophie

last: Thomson

first: Derek

first: J

middle: R

last: Highley

first: Thomas

last: Becker

first: Catherine

middle: G

middle: H

last: Gillingwater


title: GRHL3 chromatin binding and the super-enhancer landscape are reorganized in different functional states of epidermal keratinocytes

status: Public on Apr 12 2017

city: Irvine

first: Bogi

last: Andersen

state: CA

address: 839 Health Sciences Dr.

department: Medicine

country: USA

institute: University of California, Irvine

summary: While the genomic mechanisms underlying progressive, irreversible cell lineage commitments are well-studied, we know little about the chromatin changes during transient cell states such as cell migration. Interestingly, a large number of SEs in NHEK-D and NHEK-M overlap genes encoding transcription factors with important roles in promotion of epidermal differentiation, including GRHL3, TP63, RUNX1, NOTCH3 and FOS. To test the role of these SE-associated transcription factors in a systematic manner, and to place GRHL3 in the context of other keratinocyte differentiation regulators, we used siRNAs to individually knock down GRHL3 and 50 other transcriptional regulators in NHEK-D. These transcriptional regulators were selected based on expression changes during human keratinocyte differentiation. Many have been previously implicated in epidermal differentiation in mice and humans; the genes encoding 22 of them are associated with SEs. To assess the effect of the knockdowns on keratinocyte differentiation, we monitored the expression of approximately 14,000 genes with custom-made Agilent microarrays. Among the 14,000 genes whose expression we monitored were all genes expressed in human keratinocytes and all transcriptional regulators. This 51 x 14,000 gene expression matrix provided a rich dataset to explore gene regulatory networks in epidermal differentiation.

overall_design: 50 transcription factors with known or suspected roles in epidermal differentiation were selected for siRNA knockdown. Each factor showed a significant change in expression during epidermal differentiation and had a well-defined DNA binding motif. Pooled siRNA for each factor (Dharmacon) were used for knockdown in NHEK. 24 hours after knockdown, cells were induced to differentiate by the addition of high calcium media, and collected 24 hours later. RNA was extracted and run on custom designed arrays. Each factor was knocked down as a single replicate, and four samples of scramble control siRNA were also included for comparison. Differential gene expression was determined by CyberT. R was used for PCA analysis, and hierarchical clustering of the data. Gene Enrichment Analysis was performed using GSEA.  Weighted Gene Correlation Analysis (WGCNA) was used to develop network level descriptions of the siRNA data, and to link factors to the genes they are predicted to regulate. Analysis was limited to genes that showed differential expression across epidermal differentiation.

first: Rachel

last: Herndon-Klein

first: Amelia

middle: S

last: Hopkin


title: Gene expression changes in adult mouse cardiomyocytes when Brg1 and Brm are knocked out

city: Chapel Hill

first: Scott

last: Bultman

state: NC

department: Department of Pathology and Laboratory Medicine; Department of Genetics

institute: University of North Carolina at Chapel Hill

summary: Identification of gene expression changes in wild type versus mutant mouse hearts where Brg1 and Brm were knocked out in adult cardiomyocytes.

overall_design: A Tamoxifen induced knock out of Brg1 in Brm null MHC Cre-ERT mice created the double knock out in adult mouse cardiomyocytes.  Agilent Sure Print G3 Mouse Gene Expression one color (Cy3) microarray platform was utilized to compare 4 wild type and 4 control cDNA samples.

first: Monte

last: Willis


title: External factors inducing metabolic adaptations in white adipose tissue in wildtype C57BL/6J mice housed at thermoneutrality.

status: Public on Apr 06 2017

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University


title: Genome wide expression analysis of FACS-isolated Shp2 mutant neonatal myogenic progenitor cells

city: Berlin

first: Joscha

last: Griger

address: Robert-Rössle-Strasse 10

country: Germany

institute: Max Delbrück Centre for Molecular Medicine

summary: The equilibrium between proliferation and quiescence of myogenic progenitor and stem cells is tightly regulated to ensure appropriate muscle growth and repair. The non-receptor tyrosine phosphatase Shp2 (Ptpn11) is an important transducer of growth factor and cytokine signaling. Here we combined complex genetic analyses, biochemical studies and pharmacological interference to demonstrate a central role of Shp2 in postnatal myogenesis of mice. Loss of Shp2 drove muscle stem cells into quiescence during postnatal muscle growth and repair and thus interfered with myogenesis in a drastic manner. This Shp2 function was observed in postnatal but not fetal myogenic stem cells. Thus, we provide evidence for an unexpected molecular difference in the control of proliferation and cell cycle withdrawal in fetal and postnatal myogenic stem cells.

overall_design: Total RNA was obtained from VCAM1+CD31-CD45-Sca1- cells isolated from newborn control and coShp2 mice (P0) by FACS


title: Temperature-flux induced metabolic adjustments in WAT

summary: Mice have their lowest (basal) metabolic rate when housed at thermoneutrality, which starts above 29 degrees C. Although they eat less, and thus reduce their energy intake, their energy balance remains positive leading to an increased adiposity, especially when fed a high fat diet. However, almost all metabolic mouse studies are performed at standard room temperatures ranging between 20 and 22 degrees C. Previously, we showed that housing mice at thermoneutrality lead to massive increased adiposity, while metabolic dysfunction of white adipose tissue (WAT) was absent. Here, we  studied whether an increased metabolic flux through WAT induces cellular stress and underlies tissue dysfunction leading to tissue inflammation.  C57BL/6JOlaHsd wildtype male mice, aged 9 weeks, were fed purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks to acclimatize, followed by 12 weeks a BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C). Subsequently, mice were divided into different treatment groups: i) control group, which remained at thermoneutrality for 5 days, ii) 5 days normal housing temperature (22 C degrees) while housed continously in an indirect calorimetry system. At the end of the study, after 2 hours food removal at the start of the light phase, mice were killed immediately by decapitation after taking them out of the indirect calorimetry system. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 8x60K microarrays.

overall_design: C57BL/6JOlaHsd wildtype male mice, aged 9 weeks, were fed purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks to acclimatize, followed by 12 weeks a BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C). Subsequently, mice were divided into different treatment groups: i) control group, which remained at thermoneutrality for 5 days, ii) 5 days normal housing temperature (22 C degrees) while housed continously in an indirect calorimetry system. Mice were killed immediately after taking them out of the indirect calorimetry system by decapitation after 2 hours food removal at the start of the light phase. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 8x60K microarrays.

first: F

last: Hoevenaars

first: E

first: I

last: van der Stelt

last: Keijer


title: DFO-induced hypoxia leading to metabolic dysfunction in WAT

summary: Metabolic dysfunction of white adipose tissue (WAT) is considered to be underlying the comorbidities in obesity, including insulin resistance and tissue inflammation. Moreover, due to the expansion of WAT, local tissue hypoxia has been reported. Whether local tissue hypoxia underlies the metabolic de-arrangements and is the first step in initiation inflammation is questioned here. Desferrioxamine (DFO) is a chemical compound trapping free iron, thus leading to a reduction in oxygen availability within the body, which mimics hypoxia. Therefore, C57BL/6JOlaHsd wildtype male mice, aged 9 weeks, were fed purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks to acclimatize, followed by 12 weeks a BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C) to induce massive expansion of WAT without metabolic dysregulation (Hoevenaars et al., Mol Nutr Food Res 2014). Subsequently, mice were divided into different treatment groups: i) control group, ii) 5 days Desferrioxamine (DFO) daily injections (100 mg/kg body weight). Mice were killed by decapitation at the end of the experiment after 2 hour food removal at the start of the light phase. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 8x60K microarrays.

overall_design: C57BL/6JOlaHsd wildtype male mice, aged 9 weeks, were fed purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks to acclimatize, followed by 12 weeks a BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C). Subsequently, mice were divided into different treatment groups: i) control group, ii) 5 days Desferrioxamine (DFO) daily injections (100 mg/kg body weight). Mice were killed by decapitation at the end of the experiment after 2 hour food removal at the start of the light phase. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 8x60K microarrays.


title: Identification of a Mammalian Silicon Transporter

status: Public on Apr 05 2017

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

summary: Silicon (Si) has long been known to play a major physiological role in certain organisms, including some sponges and many diatoms and higher plants, leading to the recent identification of multiple proteins responsible for silicon transport in a range of algal and plant species. In mammals, despite several convincing studies suggesting that silicon is an important factor in bone development and connective tissue health, there is a critical lack of understanding in biochemical pathways that enable silicon homeostasis.  Here we report the identification of a mammalian efflux silicon transporter, namely Slc34a2 (also known as NaPiIIb), which was upregulated in the kidneys of rats following chronic dietary silicon deprivation. When heterologously expressed in Xenopus laevis oocytes, the protein displayed marked silicon transport activity, specifically efflux, comparable to plant OsLsi2 transfected in the same fashion and independent of sodium and/or phosphate influx. This is the first evidence for a specific active transporter protein for silicon in mammals and suggests an important role for silicon in vertebrates.

overall_design: Gene arrays were performed on kidney samples from rats after chronic dietary silicon deprivation and differences were sought for the regulation of potential transporters.

first: Sarah

last: Ratcliffe

first: Ravin

last: Jugdaohsingh

first: Jian

middle: F

last: Ma

first: Nakimi

last: Mitani-Ueno

first: Julien

last: Vivancos

first: Rupesh

last: Deshmukh

first: Mark

middle: V

last: Boekschoten

first: Michael

last: Müller

first: Robert

last: Mawhinney

first: Alan

last: Marron

first: Paul

last: Isenring

first: Stephen

last: Kinrade

first: Richard

last: Bélanger

first: Jonathan

last: Powell


title: miRNA profiling in primary human peritoneal mesothelial cells (HPMCs) and TGF-β1-stimulated

city: Cardiff

first: Donald

middle: James

last: Fraser

state: Wales

address: Heath Park Campus

department: School of Medicine

institute: Cardiff University

summary: TORAY microarray assays were performed on HPMCs derived from four independent donors. miRNA expression was measured in control samples and after 1 ng/ml of TGF-β1 treatment for 48 h. TGF-β1-driven mesothelial-to-mesenchymal transition (MMT) was confirmed in all samples by analysis of the eight molecular markers previously described (data not shown). A total of 1 μg in a volume of ≤2 μl of total RNA from each sample was subsequently used for Toray microarray analysis, performed by Central Biotechnology Services at Cardiff University.

first: Melisa

last: Lopez-Anton


title: Single-Cell analysis of human iPS-derived Cells Undergoing Endothelial-to-Hematopoietic Transition

status: Public on Apr 04 2017

city: Lund

first: Carolina

last: Guibentif

country: Sweden

institute: Lund University

summary:
In order to dissect Endothelial-to-Hematopoietic Transition (EHT) in human iPS differentiated cultures, at day ten of differentiation towards the hematopoietic lineage, CD34+ single cells were sorted
and analysed by single-cell qRT-PCR for 91 genes selected from the publication record, related to endothelium and hematopoietic stem and progenitor cells, as well as to the EHT in mouse and human.

overall_design: To ensure a good representation of both endothelial and hematopoietic fractions, each 96-well plate received equal numbers of CD43 +/- cells, using near overlapping gates. A total of 437 CD34+ single-cells sorted in 5 different plates were analysed. Following reverse transcription and pre-amplification, the samples were diluted 1:5 and run in Fluidigm 96:96 arrays on a Biomark device. 10 cell controls, no RT controls and no Template controls were run in parallel

first: Roger

last: Rönn

first: Charlotta

last: Böiers

first: Stefan

last: Lang

first: Shobhit

last: Saxena

first: Shamit

last: Soneji

first: Tariq

last: Enver

first: Göran

last: Karlsson

first: Niels-Bjarne

last: Woods


title: miRNA data in human placentas from normal pregnancies and from pregnancies complicated by SGA and IUGR [miRNA-4]

status: Public on Apr 01 2017

city: Los Angeles

first: Alison

last: Chu

address: 10833 LeConte Avenue

institute: UCLA

summary:
Placental insufficiency leading to intrauterine growth restriction demonstrates perturbed gene expression affecting placental angiogenesis and nutrient transfer from mother to fetus. To understand the post-transcriptional mechanisms underlying such placental gene expression changes, our objective was to identify key non-coding microRNAs that express biological function. To this end, we undertook microarray targeting microRNAs in placentas of appropriate (AGA, n=3) versus small for gestational age (SGA, n=3) weight infants and observed upregulation of 97 miRs in SGA versus AGA. In a larger cohort of samples, we validated by qRT-PCR, differential expression of three specific microRNAs that target genes mediating angiogenesis and nutrient transfer. This dataset was used to verify initial studies.
We performed a second microarray on a small cohort of samples in order to validate differential expression in pathways involved with angiogenesis and nutrient transfer, essential processes for placental function that when perturbed, may result in intrauterine growth restriction.

overall_design: Human placental samples were obtained immediately post-parturient. There were seven samples from the AGA group (Bw>10% and <90%) and six samples from the SGA/IUGR (Birthweight <10%) group. All placental samples were from term, singleton pregnancies.

first: Sherin

middle: U

last: Devaskar


title: An In Vitro Versus In Vivo Toxicogenomics Investigation of Pre-natal Exposures to Tobacco Smoke [Dams, Prenatal offspring]

status: Public on Apr 03 2017

first: Iain

last: Perry

state: South Glamorgan

address: Longwood Drive

department: Wales Gene Park

summary: Pregnant mice (Dams) were exposed to cigarette smoke or filtered air. Lung tissue and RNA were harvested from the lungs of the Dams and their offspring and underwent transcriptomic analysis.

overall_design: Two-condition experiment, Cigarette smoke vs. filtered air. 3 biological replicates for each condition of Dam female mice and Prenatal offspring mice.

first: Keith

last: Sexton

first: Zoe

last: Prytherch

first: Jason

last: Blum

first: Judith

last: Zelikoff

first: Kelly

last: BeruBe


title: Classification of pediatric acute myeloid leukemia based on miRNA expression profiles

city: Rotterdam

first: Askar

last: Obulkasim

state: Zuid Holland

address: Wytemaweg 80

department: Pediatric Oncology

institute: ErasmusMC - Sophia Children's Hospital

summary: Pediatric acute myeloid leukemia (AML) is a heterogeneous disease with respect to biology as well as outcome. In this study, we investigated whether known biological subgroups of pediatric AML are reflected by a common microRNA (miRNA) expression pattern. We assayed 665 miRNAs in 165 pediatric AML samples. First, unsupervised clustering was performed to identify patient clusters with common miRNA expression profiles. Our analysis unraveled 14 clusters, seven of which had a known (cyto-)genetic denominator. Finally, a robust classifier was constructed to discriminate six known molecular aberration groups: 11q23-rearrangements, t(8;21)(q22;q22), inv(16)(p13q22), t(15;17)(q21;q22), NPM1 and CEBPA mutations. The classifier achieved accuracies of 89%, 95%, 95%, 98%, 91% and 96%, respectively. Although lower sensitivities were obtained for the NPM1 and CEBPA (32% and 66%), relatively high sensitivities (84%-94%) were attained for the rest. Specificity was high in all groups (87%-100%). Due to a robust double-loop cross validation procedure we employed, the classifier only used expression of 47 miRNAs to generate the aforementioned accuracies. To validate the 47 miRNA signatures, we applied them to a publicly available adult AML dataset. Despite partial overlap of miRNA platforms and known molecular differences between pediatric and adult AML, the signatures performed reasonably well. This corroborates our claim that the reported miRNA signatures are not dominated by sample size bias in the pediatric AML dataset. We conclude that cytogenetic subtypes of pediatric AML have distinct miRNA expression patterns. Note that, reproducibility of the miRNA signatures in adult dataset suggests that the respective aberrations have a similar biology both in pediatric and adult AML

overall_design: Viably frozen diagnostic bone marrow or peripheral blood samples from 165 de novo pediatric AML cases were provided by the Dutch Childhood Oncology Group, the AML ‘Berlin-Frankfurt-Münster’ Study Group, the Czech Pediatric Hematology Group and the St. Louis Hospital in Paris, France. Samples represented the most common and relevant cytogenetic groups and were selected based on the availability of high-quality RNA. Informed consent was obtained from all patients, after Institutional Review Board approval, according to national law and regulations. Samples were enriched to contain at least 80% leukemic cells as previously described23. Routine analysis of recurrent non-random cytogenetic aberrations was performed by standard chromosome banding analysis, RT-PCR, and split-signal FISH (MLL-rearrangements, inv(16)(p13q22), t(8;21)(q22;q22), t(15;17)(q21;q22), t(7;12)(q36;p13), t(8;16)(p11;p13), and NUP98-rearrangements) and hotspot mutations in genes (NPM1, CEBPA, FLT3-ITD, NRAS, KRAS, PTPN11, c-KIT, and MLL-PTD). MicroRNA expression profiling was performed by Taqman® Array MicroRNA Cards v2.0 (Applied Biosystems, Foster City, CA, USA). Raw Ct-values were analyzed, summarized and exported using SDS 2.3 (Applied Biosystems). All further biostatistical analyses including quality control, aggregation of data, data normalization, and filtering were performed using R 2.11.1.

first: Maarten

last: Fornerod


title: Galectin-3 binding protein (Gal-3BP), coronary artery disease and cardiovascular mortality – insights from the LURIC study

city: Eggenfelden

first: Christian

middle: Albert

last: Gleissner

address: Simonsöder Allee 20

department: Cardiology

institute: Rottal-Inn Kliniken KU

summary: Gal-3BP effects on human monocyte-derived macrophages were assessed in vitro. Macrophages were treated with recombinant human Gal-3BP or control buffer and gene expression was measured using Illumina Sentrix-8 gene arrays. Gene array data were analyzed with the Local pooled error (LPE). There was significant regulation of 217 probe sets corresponding to 200 genes (115 up, 85 down). Analysis of the significantly upregulated genes identified “inflammatory/immune response” as one of the most strongly regulated gene ontologies. Our finding that Gal-3BP induces genes and proteins involved in immune and inflammatory response in human monocyte-derived macrophages is in line with previously published data on the role of human Gal-3BP.

overall_design: Effects of Galectin-3 binding protein on human monocyte-derived macrophages were assessed (n=2 per group).


title: Prepartal energy intake alters blood polymorphonuclear leukocyte transcriptome during the peripartal period in Holstein cows

status: Public on Mar 31 2017

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

institute: University of Illinois at Urbana-Champaign

summary: Using an Agilent microarray platform, the present study examined changes in the transcriptome of bovine polymorphonuclear leukocytes (PMNL) due to prepartal dietary intake.  Twelve Holstein cows were fed a high-straw, control diet (CON; NEL = 1.34 Mcal/kg) or overfed a moderate-energy diet (OVE; NEL = 1.62 Mcal/kg) during the dry period.  Blood for PMNL isolation and metabolite analysis was collected at -14 and +7 d relative to parturition.  At an ANOVA false discovery rate (FDR) <0.05, energy intake (OVE vs. CON) influenced 1806 genes.  Dynamic Impact Approach (DIA) bioinformatics analysis classified treatment effects on KEGG pathways, including: activated Oxidative Phosphorylation and Biosynthesis of Unsaturated Fatty Acids, and inhibited RNA Polymerase, Proteasome, and Toll-like Receptor Signaling Pathway.  This analysis indicates that processes critical for energy metabolism and cellular and immune function were impacted with mixed results.  However, overall interpretation of the transcriptome data agreed in part with literature documenting a potentially detrimental, chronic activation of PMNL in response to overfeeding.  The widespread, transcriptome-level changes captured here confirm the importance of dietary energy adjustments around calving on the immune system.

overall_design: 8 cows were assigned to one of two groups which differed in dietary energy levels fed throughout the 45-d dry period.  One group received at least 100% calculated NEL (CON; 1.34 Mcal/kg DM) from a diet high in wheat straw while the other received over 140% calculated NEL (OVE; 1.62 Mcal/kg DM) from a corn silage-based diet. Total RNA from PMNL isolated from coccygeal venous or arterial blood samples (~120 mL)  collected in vacutainer tubes containing acid citrate dextrose (ACD Solution A; Fisher Scientific) on days -14 (±2) and +7 relative to parturition.

first: A

last: Agrawal

first: M

middle: J

last: Khan

first: D

middle: E

last: Graugnard

last: Vailati-Riboni

first: S

middle: L

last: Rodriguez-Zas

first: J

last: Osorio

last: Loor


title: HCV dynamics and cellular gene expression in uPA-SCID chimeric mice with humanized livers during intravenous silibinin monotherapy

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
Background/Aim: Legalon SIL (SIL) is a chemically hydrophilized version of silibinin that has exhibited hepatoprotective and antiviral effectiveness against hepatitis C virus (HCV) in patients leading to viral clearance in combination with ribavirin. To elucidate the incompletely understood mode of action of SIL against HCV, we studied viral response kinetics and cellular gene expression during SIL treatment in the absence of an adaptive immune response in uPA-SCID chimeric mice with humanized livers.

Methods: Chronically HCV-infected mice were treated with daily intravenous SIL at 469 mg/kg (n=5), 265 mg/kg (n=5) or 61.5 mg/kg (n=5). Serum HCV and human albumin (hAlb) were measured frequently and liver HCV RNA was analyzed at days 3 and 14. Microarray analysis of human hepatocyte gene expression was performed at days 0, 3, and 14 of treatment. Mathematical modeling was used to estimate viral kinetic parameters and SIL effectiveness.

Results: While hAlb remained constant, a biphasic viral decline in serum was observed consisting of a rapid 1st phase followed by a 2nd slower (or plateau with the two lower SIL dosing) phase. SIL effectiveness in blocking viral production was similar among dosing groups (median =77%). However, the rate of HCV-infected hepatocyte decline, δ, was dose-dependent. Intracellular HCV RNA levels correlated (r=0.66, P=.01) with serum HCV RNA. Pathway analysis revealed increased anti-inflammatory and anti-proliferative gene expression in human hepatocytes in SIL-treated mice.

Conclusions: The results suggest that SIL could lead to a continuous 2nd phase viral decline, i.e., potentially viral clearance, in the absence of adaptive immune response along with increased anti-inflammatory and anti-proliferative gene expression in human hepatocytes.

overall_design: In this study, 6 human hepatocyte chimeric mice were treated with SIL and sacrificed at either 3 or 14 days after treatment. An additional 3 mice were used as controls. Human hepatocytes were finely dissected, and total RNA was extracted for microarray analysis to examine the effect of SIL on gene expression over time.

first: Swati

last: DebRoy

first: Nobuhiko

last: Hiraga

first: Michio

last: Imamura

first: C

middle: N

last: Hayes

first: Sakura

last: Akamatsu

first: Laetitia

last: Canini

first: Alan

last: Perelson

first: Ralf

middle: T

last: Pohl

first: Stefano

last: Persiani

first: Susan

last: Uprichard

first: Chise

last: Tateno

first: Harel

last: Dahari

first: Kazuaki

last: Chayama


title: Gene expression analysis of RACB-transgenic barley plant lines in interaction with Blumeria graminis f.sp. hordei

status: Public on Mar 27 2017

city: Freising

first: Ralph

last: Hueckelhoven

department: Chair of Phytopathology

institute: TU München

summary: To analyze RACB- and Bgh (Blumeria graminis f.sp. hordei)-dependently expressed genes we used wild type and transgenic barley misexpressing the susceptibility factor RACB

overall_design: Gene expression was analyzed at 12 hours post infection (hpi) and 32 hpi in untreated and Bgh-treated samples in three plant lines (wild type (WT); expressing constitutively activated (CA) RACB; RNAi RACB). In total 4 biological replicats were performed.

first: Vera

last: Schnepf

last: Hückelhoven


title: Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Department of Regenerative Biology

institute: University of Wisconsin

type: Genome binding/occupancy profiling by array

summary: During cell fate transitions the chromatin organization of the precursor cell changes from that of the endpoint cell. Current computational approaches to analyze chromatin modifications across multiple cell types do not model how the cell types are related on a lineage or over time. To overcome this limitation, we have developed a method called CMINT (Chromatin Module INference on Trees), a probabilistic clustering approach to systematically capture chromatin state dynamics across multiple cell types. Using the output from CMINT we gained novel insights into chromatin state dynamics of reprogramming to induced pluripotent stem cells (iPSCs.) We found that chromatin changes could occur without large gene expression changes; different combinations of activating marks were associated with specific reprogramming factors; in partially reprogrammed cells there was an order of acquisition of chromatin marks at pluripotency loci; and multivalent states, comprising previously undetermined combinations of activating and repressive histone modifications, were enriched for an architectural protein.

overall_design: ChIP on chip was performed on mouse embryonic fibroblasts (MEFs), partially reprogrammed cells (pre-iPSCs) and completely reprogrammed cells (iPSCs)


title: Mouse ES Cells: Control vs Hottip_VP160 and Hoxa13

status: Public on Mar 10 2017

city: London

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

institute: Queen Mary University of London

summary: Transcriptional profiling of mouse embryonic stem cells comparing control (dCas9 transfected) ES cells with ES cells transfected with a Hottip promoter gRNAs and Hoxa13 promoter gRNAs along with dCAs9-VP160.  Goal was to determine the effects of activation of Hottip lncRNA and Hoxa13 on expression of Hox genes

overall_design: Two-condition experiment, Control ES (3 biological replicates) vs. ES cells tranfected with dCas9-VP160 for Hottip (4 biological replicates) and Hoxa13 (3 biological replicates).

first: Graeme

last: Grimes


title: Selective estrogen receptor modulator-like gene expression in prepubertal rat testis after soy feeding

status: Public on Feb 02 2017

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: In this study, we investigated the potential estrogenicity of soy protein isolate (SPI) as opposed to pure isoflavones (i.e., estradiol) in the prepubertal stage of testis development. Bioinformatics analysis of the microarray analysis indicate that rather than acting as a weak estrogen in the developing testis, SPI appears to act as a selective estrogen receptor modulator with little effect on reproductive processes.

overall_design: Weanling male Sprague-Dawley rats were fed with a semi-purified diet with casein or SPI from postnatal day 21 to 33. Additional groups were feed with casein or SPI and treated s.c. with 10 ug/kg/d estradiol via osmotic minipump.

first: Martin

last: Ronis

first: Kartik

last: Shankar

first: Neha

last: Sharma

first: Michael

last: Blackburn

first: Rohit

last: Singhal

first: Kelly

last: Mercer

first: Thomas

last: Badger


title: Tongue tissue gene profile in 4NQO induced tongue carcinogenesis before and after IL-1Ra interference

status: Public on Feb 11 2017

city: Guangzhou

first: Tong

last: Wu

state: Guangdong

address: Zhongshaner Road

country: China

institute: Sun Yat-sen University

summary: Nine groups of rat tongue tissue RNA samples, including three from normal control, three from 4NQO induced tongue tissue, and three from 4NQO induced and IL-1Ra interference tongue tissue (3 rats per group) were collected for gene microarray hybridization.

overall_design: Significant fold changes among genes were determined by taking the ratio of the expression between 4NQO group and 4NQO+IL-1Ra group versus normal control group in epithelia and fibroblasts cells


title: Transcriptomic responses of the liver and adipose tissues to altered carbohydrate-fat ratio in diet: An isoenergetic study in young rats

status: Public on Mar 24 2017

city: Takasaki

first: Toshitada

last: Nagai

state: Gunma

address: 37-1 Nakaorui-machi

department: Department of Food and Life-Science

institute: Takasaki University of Health and Welfare

summary:
To elucidate the effects of altered dietary carbohydrate and fat balance on liver and adipose tissue transcriptomes,
3-week-old rats were fed three kind of diets: low, moderate and high fat diets (L, M and H) containing a different ratio of carbohydrate:fat (C:F) (65:15, 60:20 and 35:45 in energy percent, respectively).

overall_design: Rats consumed the diets for 9 weeks, and were subjected to biochemical and DNA -microarray analyses.

first: Mitsuru

last: Tanaka

first: Akihito

last: Yasuoka

first: Manae

last: Shimizu

first: Yoshikazu

last: Saito

first: Kei

last: Kumakura

first: Tomiko

last: Asakura


title: Pyruvate kinase M1 and M2 isoform knock in ES cells differentiate into three germ layers

status: Public on Mar 08 2017

city: Suita

first: Masamitsu

last: Konno

state: Osaka

address: Yamadaoka 2-2

institute: Osaka Univ.

summary: Analysis of wild type, PKm1 KI, and PKm2 KI ES cells.

overall_design: Each ES cells were differentiated into three germ layer using embryoid body formation culture. Total RNAs were isolated from embryoid body at day 0, 3, and 7

first: Hideshi

last: Ishii


title: Analysis of gene expression signatures between bone marrow derived dendritic cells generated from Wild type or DCIR(Clec4a2) knockout mice infected or not with Mycobacterium tuberculosis

status: Public on Jan 10 2017

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

summary: To further analysis of our gene expression approach, we have employed whole mouse genome microarray expression profiling as a discovery platform to identify genes which are modulated in bone marrow derived dendritic cells (BMDCs) which expressed or not the receptor DCIR (Clec4a2).  BMDC were obtained from wild type mice or DCIR Knockout mice, and after 7 days of culture, the cells were infected or not with Mycobacterium tuberculosis at a multiplicity of infection of 3 bacteria/cell. A downmodulation of some interferon responsive genes was identified in knock out cells compare to the wild type, in particular in steady state condition and following 4h of infection with the bacteria.

overall_design: Gene expression in BMDCs was measured at 0, 4 and 18h after infection with Mycobacterium tuberculosis at a Multiplicity Of Infection (MOI) of 3 bacteria/cell.  Four independent experiments were performed at each time point (0, 4 and 18 hours) using different mice for each experiment.

first: Anthony

last: Troegeler

first: Ingrid

last: Mercier

first: Olivier

last: Neyrolles


title: EC-tagging experiments

status: Public on Feb 01 2017

city: Merced

first: Michael

last: Cleary

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

summary: whole larvae (all tissues) and tissue-specific transcriptome profiling by EC-tagging

overall_design: Whole larvae (all tissues) tagged EU-RNA was purified from larvae fed 5Eud.  Neural + imaginal disc EU-RNA was purified from 12B08>CD:UPRT larvae fed 5EC.  Mushroom body EU-RNA was purified from MB247>CD:UPRT larvae fed 5EC.

first: Mike


title: Molecular signatures of clinically tested vaccine adjuvants

status: Public on Jan 09 2017

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

institute: MPIIB

summary: Differential gene expression in mouse whole blood and lymph nodes at 4 different timepoints following administration of different vaccine/adjuvants combinations

overall_design: Gene expression analysis of whole blood and lymph node RNA following vaccine/adjuvants treatment

first: Thorunn

last: Olafsdottir

first: Intawat

last: Nookaew

first: Hans

last: Mollenkopf

first: Stefan

last: Kaufmann

first: Ali

last: Harandi


title: Jmjd2a +/+ vs -/- Pituitary microarray

status: Public on Dec 31 2016

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

summary: To understand the nature of gene expression differences between wildtype and Jmjd2a knockout females in the mouse pituitary - we performed a microarray on RNA isolated from the pituitary tissue in females who had been induced to kickstart their oestrus cycles. All females (3 per group, virgin and sexually mature) were introduced to the dirty bedding of the same stud male to control for pheromone differences. 24 hours later, the animals were sacrificed by cerival dislocation and pitutiary was harvested. RNA was extracted from the tissue and quality was checked using Bioanalyzer. All RNAs possess RIN quality score of 9.5 or above (10 in most cases). From the resulting data 5 downregulated and 3 upregulated genes were validated by qRT-PCR. While there was expected biological variation to certain degree among individuals, there was a clear distinction in sample clustering between control and knockout samples and good correlation among individual sample genotypes. Of the  downregulated genes, two were using immunoblotting on protein extracts isolated from a pool of five pitutiaries derived from females of each genotype subjected to the same experimental design. Briefly,as asummary we observe a strong prominent downregulation of  immediate early genes.

overall_design: Virgin mature (8 week age) control and knockout Jmjd2a females were oestrus cycle activated by exposure to dirty bedding of the same stud male (Whitten Effect). Then these females were sacrificed exactly 24 hours later by cervical dislocation and pitutiary tissue was dissected and harvested, washed with PBS and collected in individual eppendorf tubes and frozen in dry ice. The samples were subjected to RNA extraction using the commercial Qiagen RNAeasy kit.

first: Frederik

middle: O

last: Bagger


title: Gene expression profiles in the striatum of the R6/2 mouse model of Huntington's disease injected with LNA-oligonucleotides complementary to the CAG repeats (LNA-CTG)

status: Public on Jan 01 2017

city: Barcelona

first: Eulalia

last: Marti

address: Dr. Aiguader 88

country: Spain

institute: Centre for Genomic Regulation

summary: We investigated gene expression signatures in the striatum of wild-type mice injected with a control/scrambeled  LNA-oligonucleotide (LNA-SCB) and R6/2 mice injected with LNA-SCB or LNA-CTG. Five mice were used per condition. Each group of mice received two consecutive intrastriatal injections of LNA-CTG or LNA-SCB (0.05 nmols per injection, separated by 3 days) at 11 weeks of age , when motor symptoms appeared in the R6/2 mice. Injection of LNA-CTG resulted in a signifficant attenuation of the R6/2 mice motor defficits, as early as one week after administration (12 weeks of age) and persisted for at least 4 additional weeks (15 weeks of age). Overal gene expression in each group was evaluated short before motor improvement was observed (5 days post-injection), to detect  gene expression changes and signalling pathway alterations underlying the benefficial effects. Gene expression was assessed with Agilent SurePrint G3 Mouse GE 8 × 60K Microarray. Target genes were validated using real-time quantitative PCR.

overall_design: 15 striatal tissue samples were analyzed, using Agilent technology: 5 wild-type, LNA-SCB samples; 5 R6/2, LNA-SCB samples; 5 R6/2, LNA-CTG samples. An internal control sample was included UMRR

first: Laura

last: Rué

first: Mónica

last: Bañez-Coronel

first: Jordi

last: Creus-Muncunill

first: Albert

last: Giralt

first: Rafael

last: Alcalá-Vida

first: Gartze

last: Mentxaka

first: Birgit

last: Kagerbauer

first: M

last: Zomeño-Abellán

first: Zeus

last: Aranda

first: Veronica

last: Venturi

first: Esther

last: Pérez-Navarro

first: Xavier

last: Estivill

first: Eulàlia

last: Martí


title: Murine Neural Stem/Progenitor Cells: Control vs.PJ34

status: Public on Dec 27 2016

city: Tondabayashi

first: Akiko

last: Okuda

address: 3-11-1 Nishikiori-kita

department: Faculty of Pharmacy

institute: Osaka Ohtani University

summary: Treatment with PARP inhibitor (PJ34) suppressed the formation of neurospheres by NSPCs of wild-type or Trp53-/- through the suppression of cell cycle progression and the induction of apoptosis.  In order to identify the genes responsible for these effects.

overall_design: Two-condition experiment, wild-type vs. Trp53-/-  cells. Biological replicates: 2 wild-type replicates, 2 Trp53-/-  replicates.

first: Masanori

last: Takehashi

first: Seigo

last: Tanaka


title: Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats [microarray]

status: Public on Dec 30 2016

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

summary: Chlorpyrifos (CPF) is an organophosphorus pesticide (OP), and one of the most widely used pesticides in the world. Metabolites of CPF and other OPs continue to be identified in the majority of human samples, even in countries such as the United States where OP use is declining (Arcury et al., 2010). The effects of repeated occupational and environmental exposures to OPs are poorly understood, although human and animal studies consistently identify neurotoxicity as the primary endpoint of concern.  Thus, occupational exposures to sublethal doses of CPF are consistently associated with problems in cognitive abilities, such as learning and memory but the biological mechanism(s) underlying this association remain speculative.  To identify potential mechanisms of CPF neurotoxicity, we employed a rat model that simulated documented CPF exposures in Egyptian agricultural workers. We quantified mRNA expression profiles in the CA1 region of the hippocampus of adult male Long Evans (LE) rats administered CPF at 3 or 10 mg/kg/d (s.c.)  for 21 days. Despite significant inhibition of cholinesterase activity by the end of the 21 d exposure period, the CPF-exposed rats displayed minimal signs of cholinergic toxicity. Distinct hippocampal mRNA and miRNA signatures were associated with CPF exposure. Toxicogenomics-based evidence identified increased expression of neuropeptide genes in the hippocampi of CPF-exposed rats, which have been shown to activate receptor-mediated signaling pathways involved in cell survival. The analysis of small non-coding RNA profiles suggested the possibility that miR132/212-mediated homeostatic regulatory pathways may also be activated by repeated exposures to CPF. These findings identify potential molecular effects that may contribute to neurobehavioral deficits.

overall_design: Adult male Long Evans rats were repeatedly exposed to subclinical doses of chlorpyrifos or vehicle control (peanut oil) for 21 consecutive days (study days 1-21). Two CPF formulations (3 or 10 mg/kg b.w./day) or an equal volume of the vehicle were administered daily by subcutaneous injection, approximately 24 h apart. On the study day 21, animals were euthanized and hippocampus tissues were collected for biochemical and transcriptomic analyses. The global RNA profiles of all test animals were obtained using the Affymetrix GeneChip microarrays. The Illumina sequencing technologies were employed to analyzed comprehensive profiles of mRNAs and small RNAs from the rats exposed to 10 mg/kg/day CPF or the unexposed control rats.

first: Young

last: Lee

first: John

middle: A

last: Lewis

first: Naissan

last: Hussainzada

first: Pamela

last: Lein

first: David

last: Jackson

first: Jonathan

middle: D

last: Stallings


title: A Bach2-Cebp gene regulatory network for the commitment of multipotent hematopoietic progenitors [expression]

status: Public on Mar 07 2017

city: Sendai

first: ari

last: itoh

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

institute: Tohoku univ.

summary: Hematopoietic stem cells and multipotent progenitors (MPPs) commitment can be tuned in response to an infection so that their differentiation is biased toward myeloid cells. Here we find that Bach2, which inhibits myeloid differentiation in common lymphoid progenitors, represses a cohort of myeloid genes and activates those linked to lymphoid function. Bach2 repressed both Cebpb and its target Csf1r, encoding C/EBPβ and macrophage colony-stimulating factor receptor (M-CSFr), respectively, whereas C/EBPβ repressed Bach2 and activated Csf1r. Bach2 and C/EBPβ further bound to overlapping regulatory regions at their myeloid target genes, suggesting the presence of a gene regulatory network (GRN) with mutual repression and antagonistic, feed-forward myeloid gene regulations. Lipopolysaccharide reduced the expression of Bach2, resulting in enhanced myeloid differentiation. The Bach2-C/EBPβ GRN pathway thus tunes MPP commitment to myeloid and lymphoid lineages under both normal conditions and after infection.

overall_design: Multipotent progenitors (MPPs) infected with  Bach2-GFP, and bzip-deletion-Bach2-GFP cultured several condition. LSK cells from wild-type (WT)  and Bach1-/- Bach2-/-  bone marrow.

first: Ari

last: Itoh-Nakadai

first: Hiroki

last: Katoh

first: Risa

last: Ebina-Shibuya

first: Kazuhiko

last: Igarashi


title: Gene expression of settled and metamorphosed Orbicella faveolata during establishment of symbiosis

status: Public on Dec 22 2016

city: University Park

first: Monica

last: Medina

state: PA

address: 218 Mueller Lab

department: Biology

institute: Pennsylvania State University

summary: Corals rely on a symbiosis with dinoflagellate algae (Symbiodinium spp.) to thrive in nutrient poor tropical oceans. However, the coral-algal symbiosis can break down during bleaching events, potentially leading to coral death. While genome-wide expression studies have shown the genes associated with the breakdown of this partnership, the full conglomerate of genes responsible for the establishment and maintenance of a healthy symbiosis remains unknown. Results from previous studies suggested little transcriptomic change associated with the establishment of symbiosis. In order to elucidate the transcriptomic response of the coral host in the presence of its associated symbiont, we utilized a comparative framework. Post-metamorphic aposymbiotic coral polyps of Orbicella faveolata were compared to symbiotic coral polyps 9 days after metamorphosis and the subsequent differential gene expression between control and treatment was quantified using cDNA microarray technology. Coral polyps exhibited differential expression of genes associated with nutrient metabolism and development, providing insight into pathways turned as a result of symbiosis driving early polyp growth. Furthermore, genes associated with lysosomal fusion were also upregulated, suggesting host regulation of symbiont densities soon after infection.

overall_design: RNA from 3 control and 3 infected polyp samples were hybridized in a 3-replicate pooled reference (6 total hyb's)

first: Aubrie

last: O'Rourke

first: Aki

last: Ohdera

first: Shinichi

last: Sunagawa

first: Erica

last: Diaz-Almeyda

first: Michael

middle: K

last: DeSalvo

first: Mary

last: Coffroth

first: Christian

last: Voolstra


title: Chloroplast redox status modulates genome-wide plant responses during plant-microbe interaction

status: Public on Dec 20 2016

city: Rosario

first: Juan

middle: José

last: Pierella Karlusich

state: Santa Fe

address: Esmeralda y Ocampo - Predio CONICET

country: Argentina

institute: Instituto de Biología Molecular y Celular de Rosario (IBR)

summary: Down-regulation of reactive oxygen species build-up in chloroplasts by expression of a plastid-targeted flavodoxin (Fld) delayed localized cell death in tobacco leaves inoculated with the non-host bacterium Xanthomonas campestris pv. vesicatoria (Xcv), while other defensive responses were unaffected. To better understand these effects we compared the transcriptomic alterations caused by Xcv inoculation on leaves of Fld-expressing tobacco plants and their wild-type siblings.

overall_design: Gene expression in tobacco leaves was measured at 19 hours after infiltration with a suspension of 10^8 CFU/ml of Xanthomonas campestris pv. vesicatoria. Control conditions were carried out infiltrating with mock solution (10 mM MgCl2). The analysed tobacco lines were the trangenic line pfld4-2, which expresses flavodoxin in their chloroplasts, and their wild type siblings. Two pooled biological replicates were used for each treatment and line.

first: Néstor

last: Carrillo

first: Mohammad-Reza

last: Hajirezaei

first: Uwe

last: Sonnewald

first: Sophia

first: Seyed

last: Hosseini

first: Fahimeh

last: Shahinnia

first: Matías

last: Zurbriggen


title: Pyelonephritis-Mediated Renal Fibrosis is Associated with Severe Inflammation

status: Public on Dec 29 2016

city: Columbus

first: Ashley

middle: R

last: Jackson

state: OH

address: 700 Children's Dr

department: Molecular and Human Genetics

institute: Nationwide Children's Hospital

summary: Despite a growing body of knowledge regarding the pathogenesis of urinary tract infection, the mechanisms of renal scaring associated with acute pyelonephritis (APN) are poorly understood.  Limited data available regarding histopathology, immune cell recruitment and gene expression changes during APN severely restricts the development of therapies to prevent renal scars.  Here, we address this knowledge gap using inbred, immunocompetent mice with vesicoureteral reflux. Transurethral inoculation of uropathogenic Escherichia coli leads to renal mucosal injury, tubulointerstitial nephritis, and interstitial fibrosis – all histopathologic features of human APN.  Interstitial fibrosis correlates most significantly with inflammation 7 and 28 days post infection.  Flow cytometry identifies recruitment of neutrophils, macrophages, and lymphocytes to infected kidneys.  Renal transcriptional analysis reveals molecular signatures associated with renal ischemia-reperfusion injury, immune cell chemotaxis, and leukocyte activation.  Thus, C3H/HeOuJ mice with APN comprise a novel model of renal fibrosis that recapitulates the human condition of acquired renal scarring in an immunocompetent setting.  The integration of organ pathology, quantitative cellular immune influx, and transcriptional analyses begin, for the first time, to define mechanisms of tissue injury during APN in the context of an intact immune response.  The strong relationship between pro-inflammatory cell recruitment and fibrosis supports the hypothesis that renal scarring arises as a consequence of excessive host inflammation.  Our studies suggest that immunomodulatory therapies should be investigated to reduce renal scarring in patients with APN.

overall_design: Gene expression was measured at baseline (n=4) and 7 days (n=4) post infection in kidneys of adult female C3H/HeOUJ mice.

first: Birong

last: Li

first: Babitha

last: Haridas

first: Hanna

last: Cortado

first: Rebecca

last: Kohnken

first: Brad

last: Bolon

first: Kirk

last: McHugh

first: Andrew

last: Schwaderer

first: John

last: Spencer

first: David

middle: S

last: Hains

first: Sheryl

last: Justice

first: Santiago

last: Partida-Sanchez

first: Brian

last: Becknell


title: RANK-Fc treatment in MMTV-PyMT late carcinoma

status: Public on Dec 19 2016

city: Hospitalet de Llobregat

first: Eva

last: González-Suárez

state: Barcelona

address: Hospital Duran i Reynals - 3a planta -Gran Via de l'Hospitalet, 199

department: Epigenetics and Cancer Biology

institute: Institut d'Investigació Biomèdica de Bellvitge

summary:
Transcriptional profile of MMTV-PyMT late carcinomas after adjuvant or neoadjuvant treatment with RANK-Fc (receptor activator of NF-kB)
cells isolated from one single MMTV-PyMT carcinoma were orthotopically injected in syngeneic WT mice, which were randomized 1:1 for neoadjuvant RANK-Fc or mock treatment (passage 1) for 4 weeks. Cells isolated from both treatment arms were pooled and injected into the fat pad of FvB recipients (passage 2) in limiting dilutions (mimicking occult disease) and again randomized 1:1 for additional RANK-Fc (adjuvant) or mock treatment

overall_design: passage 1: 2 control tumor samples (CT), 3 RANK-Fc treated tumor samples (Fc); passage 2: 2 control tumor samples (CT_CT), 3 neoadjuvant RANK-Fc treated  tumor samples (Fc_CT, pre-RANK-Fc), 3 adjuvant RANK-Fc treated  tumor samples (CT_Fc, post-RANK-Fc); 3 neoadjuvant and adjuvant RANK-Fc treated  tumor samples (FC_FC, pre&post-RANK-Fc)

last: Gonzalez-Suarez

first: Guillermo

last: Yoldi


title: Murine lung tissue: Gremlin-1 transgenic vs. wild type

status: Public on Dec 21 2016

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Transcriptional profiling of murine lung tissue comparing wild type to gremlin-1 transgenic untreated or silicon dioxide (silica)-treated for two months. Gremlin-1 transgene expression in lung type II epithelial cells under SPC promoter. Aim was to compare expression of fibrosis and inflammation associated genes.

overall_design: Four condition experiment, wild type (WT), silica-treated WT, Gremlin-1 transgenic (TG) and silica-treated TG. Agilent dual color arrays with each channel analyzed independently.

first: Katri

last: Koli


title: Myeloid Cell Expressed Proprotein Convertase FURIN Attenuates Inflammation

first: Ville

middle: Kalle Tapio

last: Kytölä

address: Finn-Medi 2, Biokatu 8

department: BioMediTech

institute: University of Tampere

summary: The proprotein convertase enzyme FURIN processes immature pro-proteins into functional end- products. FURIN is upregulated in activated immune cells and it regulates T-cell dependent peripheral tolerance and the Th1/Th2 balance. FURIN also promotes the infectivity of pathogens by activating bacterial toxins and by processing viral proteins. Here, we evaluated the role of FURIN in LysM+ myeloid cells in vivo. Mice with a conditional deletion of FURIN in their myeloid cells (LysMCre-fur(fl/fl)) were healthy and showed unchanged proportions of neutrophils and macrophages. Instead, LysMCre-fur(fl/fl) mice had elevated serum IL-1β levels and reduced numbers of splenocytes. An LPS injection resulted in accelerated mortality, elevated serum pro-inflammatory cytokines and upregulated numbers of pro-inflammatory macrophages. A genome-wide gene expression analysis revealed the overexpression of several pro-inflammatory genes in resting FURIN-deficient macrophages. Moreover, FURIN inhibited Nos2 and promoted the expression of Arg1, which implies that FURIN regulates the M1/M2-type macrophage balance. FURIN was required for the normal production of the bioactive TGF-β1 cytokine, but it inhibited the maturation of the inflammation-provoking TACE and Caspase-1 enzymes.  In conclusion, FURIN has an anti-inflammatory function in LysM+ myeloid cells in vivo.

overall_design: Two biological replicates of FURIN KO and WT peritoneal macrophages were left unstimulated or were stimulated for 1, 4 and 24 hours with LPS.

first: Zuzet

last: Cordova

first: Anna

last: Grönholm

first: Valentina

last: Taverniti

first: Sanna

last: Hämäläinen

first: Wilhelmiina

last: Niininen

first: Ilkka

last: Junttila

first: Antti

last: Ylipää

first: Matti

last: Nykter

first: Marko

last: Pesu


title: Affymetrix Chip Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (Affymetrix, mRNA, batch1)

status: Public on Dec 23 2016

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

country: Italy

institute: PICB

summary: We report the application of Affymetrix technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA),  with acupuncture, Methotrexate, Isofluorane anesthetic and placebo treatments, as well as the healthy control.

overall_design: The experiment is designed as 5 arms: epidermal needle manipulation (AP/MEC), Methotrexate injection (MTX), Isofluorane anesthetic (ANE, used as anesthesia control) and placebo (PLA, used as control) on CIA induced rheumatoid arthritis (RA) rats, as well as the normal rats (NORA, healthy control). Whole blood sampling was carried out before any therapy in RA (RA_T0) and NORA (NORA_T0) groups, and in the other groups (AP/MEC, MTX,ANE, PLA and NORA) at 1 hour and 34 days after the start of therapeutic treatments.  Finally, 24 total RNA samples (two replicates for each sampling) extracted from 24 blood samples (Peripheral blood mononuclear cells, PBMC ) were analyzed using Affymetrix microarray technology (rat230 2.0, ~31,000 probe sets, ~ 30,000 transcripts and variants from over 28,000 well-substantiated rat genes).

last: Devescovi

first: Yuanhua

last: Liu


title: Microarray analysis of aging-associated immune system alterations in the Rostral Ventral Lateral Medulla of F344 rats

status: Public on Dec 07 2016

city: El Paso

first: Sivasai

last: Balivada

state: Texas

address: 4th floor, Bioscience research building

institute: University of Texas at El Paso

summary: Progressive aging is associated with changes in sympathetic nervous system (SNS) regulation, suggesting an effect of advancing age on the functionality of central sympathetic premotor neurons.  The rostral ventral lateral medulla (RVLM) contains sympathetic premotor neurons and plays a key role in SNS regulation, and it is plausible to speculate that age-related changes in the molecular mechanisms in the RVLM may contribute to alterations in SNS regulation.  The present study tested the hypothesis that aging is associated with altered gene expression in the RVLM with emphasis on immune system associated gene transcripts.  RVLM tissue punches from young, middle-aged, and aged F344 rats were analyzed using Agilent’s whole rat genome microarray.  The RVLM gene expression profile varied with age and an association between chronological age and specific RVLM gene expression patterns was observed (p<0.05, FDR<0.3).  Functional analysis of RVLM microarray data via gene ontology profiling and pathway analysis has identified up-regulation of genes associated with immune- and stress- related responses, and down-regulation of genes associated with lipid biosynthesis and neurotransmission in aged compared with middle-aged and young rats.  Differentially expressed genes associated with complement system and microglial cells were further validated by quantitative PCR with separate RVLM samples (p<0.05, FDR<0.1).  The present results are the first to demonstrate age-related changes in the RVLM molecular mechanisms, modifications that may provide the molecular backdrop for understanding immune-associated changes in SNS regulation.

overall_design: Rostral Ventral Lateral Medulla (RVLM) tissue punches were collected from young (3 months old, 301±20 gm,n=3), middle-aged (12 months old, 423±18 gm,n=3) and aged (24 months old, 413±20 gm, n=3) male F344 rats. RNA collected from this tissue punches were analyzed using Agilent’s whole rat genome 4x44K microarray kit.

first: Chanran

last: Ganta

first: Yongqing

last: Zhang

first: Hitesh

last: Pawar

first: Richard

last: Ortiz

first: Kevin

middle: G

last: Becker

first: Arshad

last: Khan

first: Michael

last: Kenney


title: Expression data from mouse naïve (Naive), stem cell memory (TSCM), central memory (TCM) CD4+ T cells

status: Public on Dec 15 2016

city: Tokyo

first: Taisuke

last: Kondo

department: Medicine

institute: Keio University

summary:
Stem cell memory T cells can be defined as the memory T cell subsets with naïve T cell phenotypes and stem cell-like properties. We find that Notch signaling converts activated T cells into stem cell memory T (TSCM) cells by OP9-DL1 feeder cell coculture. Based on gene expression profile analysis, we provide evidence that these cells represent distinct characters with central memory T (TCM) cells and naïve T cells with effector molecules and transcription factors.
TSCM cells induced by Notch cluster closer to TCM cells than naïve T cells, and display similar phenotypes to TCM phenotype in terms of effector molecules and transcription factors, but the gene expressions of TSCM cells are entirely lower than that of TCM cells.

overall_design: For all samples, Total RNA was isolated using a ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI, USA). Microarray analysis was performed using fragmented and labeled with a Low Input Quick Amp Labeling Kit, one-color and hybridized to SurePrint G3 Mouse Gene Expression 8x60K (Agilent), all according to the respective manufacturer's instructions.

first: Rimpei

last: Morita

first: Yuumi

last: Okuzono

first: Takashi

last: Sekiya

first: Shunsuke

last: Chikuma

last: Shichita

first: Mitsuhiro

last: Kanamori

first: Masato

last: Kubo

first: Keiko

last: Koga

first: Takahiro

last: Miyazaki

first: Yoshiaki

last: Kassai


title: Gene expression analysis of ambient or 10.5% oxygen exposed rat gestation d13.5 metrial gland tissues. The animals were exposed to low oxygen from gestation day 6.5 to 13.5.

city: Kansas City

last: Soares

state: Kansas

address: 3901 Rainbow Blvd.,MS-3050

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

summary: Analysis of transcriptomic profile of metrial gland tissue in ambient (21% oxygen) and hypoxic (10.5% oxygen) conditions.

overall_design: 3 replicates of rat metrial gland tissue in ambient (21% oxygen) conditions and 3 replicates of rat metrial gland tissues in hypoxic (10.5% oxygen) conditions. Pregnant animals were exposed to 10.5% oxygen tensions from gestation day 6.5 to 13.5. Animals were sacrificed and metrial gland tissues were collected.

first: Damayanti

last: Chakraborty


title: Gene expression analysis of ambient or 0.5% oxygen exposed rat trophoblast stem (TS) cells

summary: Analysis of transcriptomic profile of TS cells grown in ambient (21% oxygen) and hypoxic (0.5% oxygen) conditions.

overall_design: 3 replicates of rat TS cells in ambient (21% oxygen) conditions and 3 replicates of rat TS cells grown under hypoxic (0.5% oxygen) conditions


title: Polysome profiling: Mouse OT-1 T cells WT vs Lck-/- (OFF)

status: Public on Nov 30 2016

city: Edinburgh

first: Thomas

last: Tan

address: Charlotte Auerbach Road

department: Institute of Immunology and Infection Research

institute: The University of Edinburgh

summary:
In order to identify gene targets of translational regulation during T cell activation, a polysome analysis was performed in a T cell receptor (TCR) transgenic model (OT-1) possessing a homogenous alpha-beta CD8 T lymphocyte population. Cells with defective TCR signal tranduction (Lck-/-, OFF) were compared to WT cells to visualise targets regulated by TCR signalling.
Total cytoplasmic ribonucleoprotein was extracted from ex vivo OT-1 transgenic T lymphocytes stimulated with SIINFEKL peptide antigen for 24h, extracts were fractionated using a sucrose density gradient, and separated into a sub-polysomal and a polysomal fraction. Total RNA from each fraction was extracted, equal volume of RNA from each fraction was individually labelled (Sub-poly: Cy3; Poly: Cy5), and hybridised onto a Agilent SurePrint G3 Mouse GE v2 8x60K Microarray.

overall_design: 4 biological replicates + dye swap control for each biological sample

first: Kate

last: Dudek

last: Sbarrato

first: Anne

last: Wiilis

first: Rose

last: Zamoyska


title: Gene expression analysis of reprogrammed pancreatic cells, liver and pancreas

status: Public on Nov 11 2016

first: Francesca M.

last: Spagnoli

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center for Molecular Medicine

summary: We recently generated pancreatic progenitor cells (so-called TiPP cells, TGIF2-induced pancreatic progenitors) by reprogramming adult hepatic cells (HEP). To analyze the extent of reprogramming and to investigate the mechanisms underlying liver-to-pancreas conversion, we analyzed the changes in gene expression in TiPP cells at two time points (day 14 and day 30 after transduction) compared to control HEP cells, mouse embryonic pancreas (E14.5) and adult pancreas and liver tissues.

overall_design: HEP cells were transduced with a lentivirus expressing TGIF2. RNA was collected 14 and 30 days after transduction from three independent biological samples. Pancreas and liver tissues were isolated from adult mice or embryos as indicated (3 independent biological samples).

first: Nuria

last: Cerdá-Esteban

first: Francesca


title: Circadian Homeostasis of Liver Metabolism Suppresses Hepatocarcinogenesis

status: Public on Nov 23 2016

city: Houston

first: Loning

last: Fu

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Chronic jet lag induces spontaneous hepatocellular carcinoma (HCC) in wild-type mice following a pathophysiological pathway very similar to that observed in obese humans. This process initiates with non-alcoholic fatty liver disease (NAFLD), progresses to steatohepatitis and fibrosis before HCC detection, and is driven by persistent genome-wide gene deregulation that induces global liver metabolic dysfunction. Nuclear receptor-controlled cholesterol/bile acid and xenobiotic metabolism are found among top deregulated pathways. Ablation of the bile acid receptor FXR dramatically increases intrahepatic bile acid levels and jet-lag-induced HCC, while loss of CAR, a well-known liver tumor promoter, inhibits NAFLD-induced hepatocarcinogenesis. Circadian disruption activates CAR by promoting cholestasis, peripheral clock disruption, and sympathetic dysfunction. Thus, FXR and CAR are clock-controlled therapeutic targets for spontaneous HCC

overall_design: Male C57BL/6 inbred Wild-type (WT) mice were single-housed and kept either in steady 12hr light/12hr dark cycles (NS) or subjected to chronic jet-lag (CJ) from 4 weeks of age between two time zones different at the time of light onset for 8 hours. Total liver RNA was isolated from control (NS) and jet-lagged (CJ) mice of 12 and 30 weeks of age at  ZT2, 10 and 18 (ZT: Zeitgeber time with light on at ZT0 and off at ZT12), snap-frozen, and used for an Agilent array. Data obtained was analyzed using the Limma Bioconductor package after normalization and batch effect removal.

first: Nicole

last: Kettner

first: Horatio

last: Voicu

first: David

last: Moore


title: Effect of prenatal ischemia on gene expression in the mouse cortex

city: Shinjuku-ku

first: Kazunori

last: Nakajima

state: Tokyo

address: 35 Shinanomachi

department: Department of Anatomy

institute: Keio University School of Medicine

summary: To determine whether preterm brain injury affects brain development, we produced ischemic brain damage in mouse embryos by occluding the maternal uterine arteries at embryonic day (E) 16.5. Then gene expression analysis was conducted using cortices from ischemic or control mice at postnatal day (P) 1.5. Results show influence of embryonic ischemia on the gene expression profiles.

overall_design: Gene expression levels in the P1.5 cortices were measured for the control or ischemic pups in which ischemia had been induced by maternal uterine artery occlusion at E16.5. Four mice in each group were analyzed.

first: Ken-ichiro

last: Kubo

first: Michihiko

last: Aramaki

first: Minkyung

last: Shin

first: Kanehiro

last: Hayashi


title: Expression data from the spinal cord of dmy rat with Mrs2 mutation

status: Public on Oct 19 2016

city: Izumisano

first: Mitsuru

last: Kuwamura

address: Rinku-Orai

institute: Osaka Prefecture University

summary:
The demyelination (dmy) rat is a unique spontaneous myelin mutation that exhibits severe myelin breakdown with a late onset of clinical signs. The causative autosomal recessive mutation has been identified at the MRS2 magnesium transporter (Mrs2) gene, which encodes an essential component of the major Mg2+ influx system in mitochondria.
To clarify the pathogenesis of myelin destruction in dmy rats, we performed a microarray analysis using spinal cord samples.

overall_design: For the microarray analysis, 6-week-old control and dmy/dmy rats were deeply euthanized. Total RNA was isolated from the cervical spinal cord with the SV Total RNA isolation system. The RNA was then prepared and hybridized to the rat Genome 230 2.0 Array (Affymetrix, Santa Clara, CA) by Bio Matrix Research, Inc. (Nagareyama, Japan.), following the protocols provided by Affymetrix.

first: M

last: Tanaka


title: Total RNA: naïve ex vivo mouse OT-1 T lymphocytes, WT vs Lck-/- (OFF)

first: Thomas

last: Tan

summary:
This experiment aims to study the transcriptome of naïve T cells at the steady state. A T cell receptor (TCR) transgenic mouse model (OT-1) posessing a homogenous alpha-beta CD8 T lymphocyte population was used, and cells with intact TCR signalling pathways (WT) were compared to those with defective signal transduction (Lck-/-, OFF).
Naïve (CD8b+, CD44low) ex vivo T cells were isolated from the superficial cervicals, axillary, brachial, mesenteric, and inguinal lymph nodes. Total RNA was extracted from the cells, labelled with Cy3, and hybridised onto an Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray.

overall_design: 3 biological replicates of WT + 4 biological replicates of Lck-/- (OFF).

first: Kate

last: Dudek


title: Severe damage on placental fetal capillary network causes mid to late fetal lethality and reduction of placental size in Peg11/Rtl1 KO mice [day 10.5]

city: bunkyou-ku

first: Moe

last: Kitazawa

address: Yusima 1-5-45

department: Medical Research Institute

institute: Tokyo Medical and Dental University

summary: Paternally expressed 11/Retrotransposon-like 1 (Peg11/Rtl1) knockout (KO) mice exhibited mid to late fetal lethality or late fetal growth retardation associated with frequent neonatal lethality. The lethal phenotype was largely dependent on genetic background and became more severe with each succeeding generation in the course of backcross experiments to C57BL/6 (B6). We previously suggested these lethal and growth phenotypes were due to severe defects in placental fetal capillaries in labyrinth layer. In this study, we reexamined KO fetuses exhibiting mid fetal lethality with internal bleeding. Importantly, basal region of fetal capillary network was specially damaged, therefore, also leading to poor expansion of the labyrinth layer and placental size reduction in later stage. Apparent up-regulation of Guanine nucleotide binding protein, alpha 2 (Gnai2) and decrement of Transmembrane protein 100 (Tmem100), Mesenchyme homeobox 2 (Meox2) and Lymphatic vessel hyaluronan Receptor 1 (LYVE1) expression were observed in earlier stage of placentas even before apparent morphological changes occurred, suggesting that these genes are involved in the maintenance of fetal capillaries associated with Peg11/Rtl1 in development.

overall_design: Gene expression profiles of WT and Peg11/Rtl1 KO placentas at day 10.5 were analyzed to identify genes involved in the maintenance of fetal capillary endothelial cells during earlier stage of the placenta.

first: Masaru

last: Tamura

first: Tomoko

last: Kaneko-Ishino

first: Fumitoshi

last: Ishino


title: Severe damage on placental fetal capillary network causes mid to late fetal lethality and reduction of placental size in Peg11/Rtl1 KO mice [day 12.5]

overall_design: Gene expression profiles of WT and Peg11/Rtl1 KO placentas at day 12.5 were analyzed to identify genes involved in the maintenance of fetal capillary endothelial cells during earlier stage of the placenta.


title: Hepatic expression data from 2-stage carcinogenesis study in rats

status: Public on Oct 24 2016

city: Osaka

first: Ko

last: Omura

address: 2-1-6 Kashima yodogawa-ku

institute: Astellas Pharma Inc.

summary:
Hepatic gene expression profiles in 2-stage carcinogenesis study were analyzed with comprehensive DNA methylation data. Combined analysis suggested that PTEN signaling and immune response such as antigen presentation was related to one side of early heapatocarcinogenesis.
We used microarrays to obtain the global gene expression profile of livers to understand the mechanism of carcinogenesis.

overall_design: Rat livers sampled at the timing of partial hepatectomy and terminal euthanasia were subjected to RN extraction and hybridization on Affymetrix microarrays. We sought to obtain hepatic gene expression data treated with various initiators and their succession. Briefly, each liver at 5w (partial hepatectomized sample) and 10w (terminal sample) from same animal were subjected to microarray analysis. MC (methylcellulose) and water mean vehicle of initiator and promoter, respectively. As an initiator, diethylnitrosamine (DEN), thioacetamide (TAA), methapyrilene (MP) and acetaminophen (APAP) were administered. As a promoter, phenobarbital (PB) was given in drinking water.

first: Takeki

last: Uehara

first: Yuji

last: Morikawa

first: Hitomi

first: Kunitoshi

last: Mitsumori

first: Keiichi

last: Minami

first: Masayuki

last: Kanki

first: Hiroshi

last: Yamada

first: Atsushi

last: Ono

first: Yasuo

last: Ohno

first: Tetsuro

last: Urushidani


title: Severe damage on placental fetal capillary network causes mid to late fetal lethality and reduction of placental size in Peg11/Rtl1 KO mice

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

overall_design: Refer to individual Series


title: Therapeutic Mechanisms of Chinese Herbal Medicine Qushi Huayu Decoction (QHD) in the Treatment of NAFLD

status: Public on Oct 01 2016

city: Shanhgai

first: Qin

last: Feng

address: 528 Zhangheng Road

department: institute of Liver diseases

institute: Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine

summary:
To understand the therapeutic mechanisms of QHD, we examined the effects of QHD treatment on the liver transcriptomes of NAFLD rats and identified multiple therapeutic targets of QHD.
We used microarrays to examine the effects of QHD and GC treatment on the liver transcriptomes of NAFLD rats induced by high fat diet and identified multiple therapeutic targets of QHD.

overall_design: Rats were randomized into 4 groups.  Rats in the control group were fed with standard chow; rats in the NAFLD group were fed with HFD


title: Role of IgD in B cell anergy

status: Public on Sep 30 2016

city: Darlinghurst

first: Christopher

middle: Carl

last: Goodnow

state: NSW

address: 384 Victoria Street

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

summary: To define the global landscape of mRNA changes in anergic B cells, and how this affected by surface IgD, mature CD93-CD23+ HEL-binding B cells were sorted from spleens of independent transgenic mice of the following genotypes: MD4, naïve B cells coexpressing IgM and IgD; MD4:ML5, anergic B cells coexpressing IgM and IgD; MM4, naive B cells expressing only IgM; MM4:ML5, anergic B cells expressing only IgM; DD6, naive B cells expressing only IgD; DD6:ML5, anergic B cells expressing only IgD.

overall_design: Spleen cells from independent mice of each genotype were sorted on each of three sorting days (sort 1, 2, 3) and frozen. RNA was isolated from all frozen samples as a single batch and labelled and hybridized as a single experiment.

middle: C


title: Dek overexpression under the environment exposed to carcinogen in oral squamous cell.

status: Public on Oct 05 2016

city: Gifu

first: Hiroyuki

last: Tomita

address: 1-1 Yanagido

institute: Gifu University

summary: Oral squamous cell carcinoma (OSCC) develop multi-step carcinogenesis, including the concept of the field cancerization. DEK gene is considered to be a proto-oncogene, has multifaceted functions, such as replication, transcription, and chromatin remodeling, and also affects oncogenic process, such as cellular proliferation, differentiation, senescence, and apoptosis. DEK overexpression has proposed to be closely associated with many malignancies, however, functional mechanisms and crucial roles are still unclear. DEK-expressing cells significantly increased in human oral squamous cell carcinogenesis. We generated ubiquitous and squamous cell-specific Doxycycline (DOX)- inducible Dek mice (iDek and iDek-e mice, respectively). DOX administrated (DOX+) iDek mice promoted field cancerization and the development of OSCC in the environment exposed to carcinogen. By the microarray expression profiling analysis, the promotion of the filed cancerization by Dek overexpression was mediated by the upregulation of DNA replication- and cell cycle (G1 to S phase transition)-related genes. Further, Dek-overexpressed tongue tumors were progressed by proliferating cell nuclear antigen (Pcna) and the elongator complex protein 3 (Elp3). Our data suggest that, by DEK overexpression enhances the carcinogenesis, including field cancerization, of OSCC stimulating the G1-to-S phase transition in the cell-cycle and DNA replication, even after carcinogen-exposed environment, and offers a fascinating target for treatment and prevention of OSCC.

overall_design: For microarray analysis, total RNA (from mouse tongue tissue) was extracted with the Simply RNA tissue Kit (Promega, Fitchburg, Wisconsin (WI), USA) on a Maxwell RSC instrument. Gene expression analysis of the RNA samples was performed using by TAKARA Bio Inc. (Shiga, Japan) using Agilent Expression Array (SurePrint G3 Mouse GE 8 × 60 K Microarray).  Two group2 (n=3 each) of Dek induced mice and Dek not induced mice

first: Takayuki

last: Nakashima


title: Total RNA: 24h activated mouse OT-1 T lymphocytes, WT vs Lck-/- (OFF)

first: Thomas

last: Tan

summary:
This experiment aims to study the transcriptome of activated T cells at 24h, using the same biological samples as the polysome profiling in GSE84781. A T cell receptor (TCR) transgenic mouse model (OT-1) posessing a homogenous alpha-beta CD8 T lymphocyte population was used, and cells with intact TCR signalling pathways (WT) were compared to those with defective signal transduction (Lck-/-, OFF).
Ex vivo OT-1 T cells were isolated from the superficial cervicals, axillary, brachial, mesenteric, and inguinal lymph nodes and then activated for 24h with cognate peptide antigen SIINFEKL. Total RNA was extracted from the cells, labelled with Cy3, and hybridised onto an Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray.

overall_design: 4 biological replicates of WT + 3 biological replicates of Lck-/- (OFF).

first: Kate

last: Dudek

last: Sbarrato

first: Anne

last: Wiilis

first: Rose

last: Zamoyska


title: Comparison of Gene expression profiling of granulosa cells treated with follicle stimulating hormone or constitutively active protein kinase A

city: Pittsburgh

first: Anthony

last: Zeleznik

address: 204 Craft Avenue

department: Obstetrics Gynecology and Reproductive Sciences

institute: University of Pittsburgh

summary: PKA activation by FSH is essential to transduce FSH-mediated effects on granulosa cell proliferation, differentiation and steroidogenesis. However, It is unknown whether activation of PKA is sufficient to account for the entire program of granulosa cell responses to FSH. We addressed this question by conducting a comprehensive comparative analysis of signaling pathways and gene expression profiles of granulosa cells stimulated with FSH or expressing a constitutively active PKA mutant, PKA-CQR.

overall_design: Undifferentiated GCs were isolated from ovaries obtained from 24 day-old female rats and cultured. The following treatments were applied: 1) EGFP lentivirus 24hr (n=2), 2) EGFP lentivirus 24h + FSH (100 ng/ml) for 24h (n=3), 3) PKA-CQR lentivirus 24h (n=3).Total RNA was extracted from the cells 24 hr. later using RNA-Bee solution, frozen at −80 C, and transported to the Genomics and Proteomics Core Laboratory of the University of Pittsburgh to perform microarray analysis with the Affymetrix Rat Genome 230 2.0 array as per the manufacturers instructions.  For data analysis, RMA normalized Affymetrix gene expression data were imported into BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for differential expression (DE) analysis. DE genes were identified using the Student t test (p<0.001) in BRB.

first: Pawan

last: Puri


title: Gene expression of skeletal muscles in response to overexpression of Notch1 intracellular domain (N1ICD)

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

summary: Analysis of gene expression profile of Tibialis anterior (TA) skeletal muscle tissues with Notch1 intracellular domain (N1ICD) overexpression. Skeletal myogenesis involves sequential activation, proliferation, self-renewal/differentiation and fusion of myogenic stem cells (satellite cells). Notch signaling is known to be essential for the maintenance of satellite cells, but its function in late-stage myogenesis, i.e. post-differentiation myocytes and post-fusion myotubes, is unknown. Here we use muscle creatine kinase (MCK)-Cre to induce N1ICD expression in multinucleated myotubes. We found that myotube-specific Notch1 activation improved muscle regeneration and exercise performance of mdx mice, a model of Duchenne Muscular Dystrophy (DMD). Agilent microarray was performed to compare gene expression in mdx control and N1ICD-overexpressing mdx muscles. The results may provide mechanistic insights into how Notch1 activation in myotubes modulate muscle function.

overall_design:
Two-condition experiment, mdx muscle vs. N1ICD-mdx muscle. Biological replicates: 3 mdx TA muscles and 3 N1ICD-mdx TA muscles.
Please note that experiments were performed technically as dual channel (eg, Cy3-labeled-mdx and Cy5-labeled-N1ICD samples hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are calculated).

first: Pengpeng

last: Bi

first: Feng

last: Yue

first: Sara

last: Wirbisky

first: Jennifer

last: Freeman


title: Gene expression in primary chondrocytes derived from Rela-cKO/control mice with/without TNF-α treatment

status: Public on Sep 15 2016

city: TOKYO

first: Taku

last: Saito

address: 7-3-1 Hongo, Bunkyo-ku

department: Orthopaedic Surgery, Faculty of Medicine

institute: The University of Tokyo

summary: To identify target genes mediating the anti-apoptotic effect of Rela, we isolated primary chondrocytes from Prrx1-Cre;Relafl/fl and Relafl/fl mice, cultured them with or without 10 ng/mL TNF-α, and compared gene expression profiles by microarray analyses.

overall_design: Primary chondrocytes from Prrx1-Cre;Relafl/fl and Relafl/fl mice were treated with or without 10 ng/mL TNF-α.

first: Hiroshi

last: Kobayashi


title: Gene expression profiling of prostate tissues and seminal vesicles from PB-Pten-NICD mice

status: Public on Sep 09 2016

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

summary: To investigate the identity of the tissue origin for metastases, we compared gene expression profiles of the prostate tissues and seminal vesicles from PB-Pten-NICD mice and those of 7 lung metastases from different mice. Three respective cell lines established from primary seminal vesicle tumors, primary prostate tumors, and lung metastases in PB-Pten-NICD mice were also included in the microarray analysis. We hypothesized that the gene expression profiles of primary and metastatic tumors should resemble those of their tissue origins. We identified genes differentially expressed between the seminal vesicle and prostate tumors. The expression profiles of the two cell lines established from primary tumors resembled those of their respective tissue origins, which supports our hypothesis. The expression profile of the metastatic cell line resembled those of the prostate tumor tissues, indicating the prostate as its tissue of origin. The expression profiles of 2 metastatic specimens each resembled those of the seminal vesicle tumors and the prostate tumors, respectively, while the expression profiles of the remaining 3 samples displayed a mixed pattern. This study suggests that metastatic tumors in this model may have originated from either the prostate, or the seminal vesicles, or both.

overall_design: Gene expression microarray analyses were performed on prostate tissues and seminal vesicles (SVs) from PB-Pten-NICD mice, on lung metastases from different mice, and on three respective cell lines established from primary seminal vesicle tumors, primary prostate tumors, and lung metastases in PB-Pten-NICD mice.

first: Li

last: Xin

first: Yiqun

last: Zhang


title: Suppression of skin tumorigenesis in CD109-deficient mice

status: Public on Sep 28 2016

city: Hiroshima

first: Shinji

last: Mii

address: 1-2-3, Kasumi, Minami-ku

department: Department of Molecular Pathology

institute: Hiroshima University Graduate School of Biomedical and Health Sciences

summary: CD109 is a glycosylphosphatidylinositol-anchored glycoprotein that is highly expressed in several types of human cancers, particularly squamous cell carcinomas. We previously reported that CD109-deficient mice exhibit epidermal hyperplasia and chronic skin inflammation. Although we found that CD109 regulates differentiation of keratinocytes in vivo, the function of CD109 in tumorigenesis remains unknown. In this study, we investigated the role of CD109 in skin tumorigenesis using a two-stage carcinogenesis model in CD109-deficient mice with chronic skin inflammation.

overall_design: We performed microarray analysis of the skin of DMBA-untreated or -treated CD109+/+ and CD109-/- mice in order to detect changes to suggest possible mechanisms for the effects

first: Masaki

last: Sunagawa


title: Binary cell fate decision as high-dimensional critical state transition

status: Public on Sep 01 2016

city: Calgary

first: Mitra

last: Mojtahedi

state: AB

address: 2500 University Dr. NW

country: Canada

institute: University of Calgary

summary: During commitment of a multipotent stem or progenitor cell to a particular lineage, a large number of genes alter their expression in a coordinated manner orchestrated by the gene regulatory network (GRN). The constraints imposed by the GRN govern how cells move in the high-dimensional gene expression state space and can be understood as a dynamical system in which phenotypic cell states (cell types) are attractors that stabilize the cell-type characteristic gene expression pattern against molecular noise. Despite insights from various theoretical models, it remains elusive how multipotent cells, when committing to a specific lineage, exit their attractor and enter a new distinct attractor. Here we show, using single-cell resolution monitoring of transcript patterns by qPCR that commitment of multipotent blood progenitor cells to either the erythroid or the myeloid lineage is preceded by a destabilization of the progenitors’ attractor state and a slowing-down of relaxation of cells from outlier states, indicating a critical state transition (“tipping point”). The high-dimensionality of the system (many genes) and availability of individual trajectories of a large ensemble of systems (many cells) affords a novel signature for critical transition which can be predicted from theory: Decrease of correlation between cells and concomitant increase of correlation between genes as the cell population approaches the tipping point. Consistent with a destabilizing bifurcation that simultaneously opens access to the erythroid and myeloid attractors, differentiation signal for either lineage caused some cells to commit to the “wrong” fate; moreover providing conflicting signals resulted in a delayed decision at the bifurcation point that however was ultimately resolved by commitment to one fate. These results suggest that the theoretical framework of “early-warning signs” and critical transitions can be applied to ensembles of high-dimensional systems, offering a formal tool for analyzing single-cell omics data beyond current descriptive computational pattern recognition.

overall_design: Mouse blood progenitor cells (EML cell line) was exposed to EPO, IL-3/GM-CSF or a mixture of both cytokines and gene expression change was measured in sorted subpopulations wrt Sca1 progenitor surface marker expression. In total, there was 4 conditions (including control), three time points (including d0) and 20 samples (10 samples in duplicates) were analyzed. Two independent experiments were performed for each condition. The untreated progenitor cell population was used as control.

first: Alexander

last: Skupin

first: Joeph

last: Zhou

first: Ivan

last: Castaño

first: Rebecca

last: Leong-Quong

first: Hannah

middle: H

last: Chang

first: Alessandro

last: Giuliani

first: Sui

last: Huang


title: Gene expression signatures in mouse epidermis with transglutaminase 1 deficiency

city: Nishinomiya

first: Kiyofumi

last: Yamanishi

state: Hyogo

address: 1-1, Mukogawa-cho

department: Department of Dermatology

institute: Hyogo College of Medicine

summary: The gene expression profile of 19.5 dpc Tgm1–/– mouse epidermis was compared with that of wild-type mice in duplicate samples, which were analyzed using microarrays. The expression of 2,502 entities was increased more than 2-fold in Tgm1–/– epidermis vs wild-type epidermis, and 1,403 of those entities corresponded to protein-coding genes. Gene ontology (GO) analysis of those entities revealed that the top 15.5% of 90 GO terms with corrected P < 0.05 were related to defense or immune responses. The entities for 177 annotated transcripts showed more than a 5-fold increase in expression in Tgm1–/– epidermis vs wild-type epidermis and those were also subjected to GO analysis. Interestingly, 24 genes from those entities were sorted into the category of defense response (P<2.78E-11; corrected P<1.50E-07).

overall_design: Gene expression was measured in  the epidermis of 19.5 dpc wild-type and transglutaminase 1 -/- mice (n=2).

first: Takashi

last: Haneda


title: Molecular Changes in the Nasal Cavity after 5 days of N, N-dimethyl-p-toluidine Exposure

status: Public on Aug 11 2016

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary:
To identify nasal cavity transcripts differentially expressed due to treatment with N, N-dimethyl-p-toluidine (DMPT), we collected RNA during the from male F344/N rats exposed to 120 mg/kg DMPT, 5 days after DMPT exposure for animals 5-6 weeks of age.  These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip Array.
A total of 2,561 gene transcripts were differentially expressed due to DMPT treatment (false discovery rate (FDR) < 0.05).

overall_design: There were 2 groups and 5x replication for each group, for 10 total samples. The groups were (1) DMPT and (2) vehicle control. We compared vehicle control vs DMPT using ORIOGEN software. The permutation based p-values for each test were significant for FDR≤5%.

first: June

last: Dunnick


title: The effect of dietary soybeans and their isoflavone content on the expression profiles of mRNAs in liver of rats

status: Public on Aug 01 2016

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

summary:
Soyfoods have been drawn the interrest in the roles that reducing risk of cardiovascular disease. Among various components, isoflavones have been come to the attention as beneficial soy ingredients. To evaluate the effectiveness of isoflavone content in dietary soybean (Glycine max) on modulating lipid metabolism, hepatic gene expressions involved in lipid metabolism were analyzed in rats. An isoflavone-rich cultivar (Yukipirika) and a conventional cultivar (Fukuyutaka) were employed. A principal component analysis (PCA) of microarray data was used to summarize characteristics of the experimental groups. As a result, the characteristics of the diets were largely explained by the first principal component (PC1). Soybean content in the diets distinctly separated in PC1. In contrast, isoflavone content had little effect on the mRNA expression.
The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.

overall_design: Male Splague-Dawley rats were randomly divided into 4 groups and fed an experimental diet for 21 days. The experimental diets were as follows: a diet containing 200 g/kg casein (Cas, n=7); a diet containing two proteins derived equally from casein and Fukuyutaka (conventional cultiver soybean) (F10, n=7); a diet containing two proteins derived from casein and Yukipirika (high-isoflavone soybean) in the proportion of three parts to one (Y05, n=7); a diet containing two proteins derived equally from casein and Yukipirika (Y10, n=8). In each of the groups, five rats with average food intake were used for microarray analysis.

first: Yoko

last: Takahashi