title: Rspo1 role in mammary gland during pregnancy

status: Public on Feb 09 2017

city: Jouy-en-Josas

first: Fabienne

last: Le Provost

address: domaine de Vilvert

institute: INRA

summary: R-spondin1 (Rspo1) is a member of a secreted protein family which has pleiotropic functions in development and stem cell growth. Rspo1 knock-out mice are sex-reversed, but some remain sub-fertile, so, they are unable to nurse their pups. A lack of Rspo1 expression in mammary epithelial cells results in an absence of duct side-branching development and defective alveolar formation. In this study we propose to characterize the molecular functions involved to mammary gland phenotype due to Rspo1 knock out. By transcriptional profiling, we have identified gene misregulated in mammary gland of Rspo1 knock-out mice during pregnancy. A stronger expression of genes characterising mesenchymal tissue was observed in the absence of alterations to the structure of mammary epithelial tissue. Mammary epithelial cell characterization, by immunohistochemistry approach, revealed a persistence of virgin markers which sign a delay in their differentiation. Moreover serial transplantation experiments show that Rspo1 is associated with a regenerative potential of mammary epithelial cell control. Our data have also highlighted that in mammary gland during pregnancy the expression of Rspo1’s partners, Lgr4 and RNF43, are negatively regulated and Tgf-β signaling is modified in the absence of Rspo1. Taken together, our results show an abrupt halt in mammary development at mid-pregnancy due to loss of further differentiated function.

overall_design: Mammary glands of eight pregnancy day-12 mice (four wild-type (WT) and four Rspo1-/- samples) and of eight other mice at pregnancy day-16 (four WT and four Rspo1-/- samples)

first: Sead

last: Chadi


title: Loss of heterozygosity drives adaptation in hybrid yeast

status: Public on Feb 21 2017

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

country: USA

institute: University of Washington

summary: CGH arrays for Smukowski Heil, et al MBE 2017. Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we address these questions using experimental evolution of de novo interspecific hybrid yeast Saccharomyces cerevisiae x Saccharomyces uvarum and their parentals.  We evolved these strains in nutrient limited conditions for hundreds of generations and sequenced the resulting cultures to identify genomic changes.  Analysis of 16 hybrid clones and 16 parental clones identified numerous point mutations, copy number changes, and loss of heterozygosity events, including species biased amplification of nutrient transporters. We focused on a particularly interesting example, in which we saw repeated loss of heterozygosity at the high affinity phosphate transporter gene PHO84 in both intra- and interspecific hybrids. Using allele replacement methods, we tested the fitness of different alleles in hybrid and S. cerevisiae strain backgrounds and found that the loss of heterozygosity is indeed the result of selection on one allele over the other in both S. cerevisiae and the hybrids. This is an example where hybrid genome resolution is driven by positive selection on existing heterozygosity, and demonstrates that even infrequent outcrossing may have lasting impacts on adaptation.

platform_organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

overall_design: Each CGH array is a comparison of the DNA content of an evolved yeast population vs the matched ancestor.

first: Chris

last: Desevo


title: Differential gene expression of dechlorinating communities with Dehalococcoides mccartyi species

status: Public on Jan 28 2017

city: Urbana

first: Yujie

last: Men

address: 205 N Mathews Ave

institute: University of Illinois at Urbana-Champaign

summary: The aim of this study is to obtain a systems level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven draft genomes were binned from the metagenomes. At an early stage (2 d), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment with exogenous cobalamin compared to the one without cobalamin addition. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid-producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted qPCR analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin. Furthermore, Dehalococcoides' corrinoid salvaging and modification pathway was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles of members of dechlorinating communities under cobalamin-limited conditions.

platform_organism:
Dehalococcoides mccartyi BAV1
Dehalococcoides mccartyi 195
Dehalococcoides mccartyi CBDB1
Dehalococcoides mccartyi VS

overall_design: Cells of dechlorinating enrichments with and without B12 were collected on 2, 9 and 13 days during TCE dechlorination process for RNA extraction, cDNA synthesis, fragmentation, labelling, and hybridization on microarray. We sought to obtain differential transcription of genes of Dehalococcoides species, in order to understand the response to B12-limited condition.

first: Ke

last: Yu

first: Jacob

last: Bælum

first: Ying

last: Gao

first: Julien

last: Tremblay

first: Emmanuel

last: Prestat

first: Ben

last: Stenuit

first: Susannah

middle: G

last: Tringe

first: Janet

last: Jansson

first: Tong

last: Zhang

first: Lisa

last: Alvarez-Cohen


title: Detailed localisation of diet-induced changes in gene expression in the murine small intestine.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: An increasing amount of evidence suggests that the small intestine may play an important role in the development of metabolic diseases, such as obesity and insulin resistance. The small intestine provides the first barrier between diet and the body. As a result, dysregulation of biological processes and secretion of signal molecules from the small intestine may be of importance in the regulation and dysregulation of whole body metabolic homeostasis. Changes in gene expression of genes involved in lipid metabolism, cell cycle and immune response may contribute to the aetiology of diet-induced obesity and insulin resistance. In the current study we present a detailed investigation on the effects a chow diet, low fat diet and high fat diet on gene expression along the proximal-to-distal axis of the murine small intestine. The reported results provide a knowledge base for upcoming studies on the role of the small intestine in the aetiology of diet-induced diseases.

overall_design: Mice were fed a chow diet, low fat diet, or high fat diet for 2 weeks whereafter the small intestine was isolated and divided in 10 equal parts. Epithelial cells were scraped off, RNA was isolated and subjected to whole genome expression profiling.

first: Nicole

last: de Wit

first: Mark

middle: V

last: Boekschoten

middle: J

first: Michael

last: Müller


title: Impact of naiR delation on the transcriptome of Streptococcus pneumoniae D39

status: Public on Feb 24 2017

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔnaiR to D39 wild type grown in CDM

overall_design: One condition design comparision of two strains including a dye swap

first: Muhammad

last: Afzal

first: Oscar

middle: P

last: Kuipers


title: Gene expression architecture of mouse dorsal and tail skin reveals functional differences in inflammation and cancer [telogen/anagen]

status: Public on Feb 27 2017

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

summary: Hair follicles are self-renewing organs within the skin which cycle through periods of growth and destruction, with an intervening period of outward quiescence. The hair follicle cycle is driven by Hedgehog and Wnt signaling and affects epithelial thickness, melanin production, immune function, and tumor susceptibility. We have previously shown that somatic alterations to the genome affect the genetic architecture of the skin. This study examines how the hair follicle cycle affects gene the genetic architecture in vivo by genomic and genetic analysis of 343 genetically heterogeneous mice during the hair follicle growth phase (anagen) and quiescent phase (telogen). We use eQTL analysis and differential correlation to identify changes in metabolic and stem cell activity not detected by differential expression. Germline influence in gene expression is profoundly higher during anagen, but this increase is not a simple factor of higher levels of gene expression. The most strongly induced eQTLs were involved in cellular energy metabolism and melanogenesis rather than hair follicle growth or hedgehog signaling. We demonstrate that hair follicle and circadian rhythm pathways are sexually dimorphic, but do not find evidence for an effect of sex on eQTL networks. We also use eQTL gene network analysis to identify candidate causal relationships between expression of genes in the hair follicle and melanin pathways, identifying Mcoln3 as a candidate for the familial melanoma locus on 1p22. To lower the bioinformatic barriers to eQTL network analysis we produced CARMEN, a free open-source stand-alone software package. This study demonstrates how to perform a systems genetic analysis of a heterogeneous tissue studied in vivo under physiologically relevant growth signals.

overall_design: A backcross of 130 samples was generated using male Mus spretus and female FVB/N mice; female F1 hybrids were mated with male FVB/N mice. Mice were aged to 7 weeks and sacrificed. Shaved dorsal skin was snap frozen.

middle: A

first: Allan

last: Balmain


title: CD54-mediated interaction with pro-inflammatory macrophages increases the immunosuppresive function of human mesenchymal stromal cells

status: Public on Jan 24 2017

city: TOULOUSE

first: Audrey

last: Varin

address: CHU Rangueil, Batiment L1, 2étage , avenue Jean Poulhès

country: France

institute: STROMALab

summary: Mesenchymal stromal cells (MSCs) sense and modulate inflammation and represent potential clinical treatment for immune disorders. However, many details of the bidirectional interaction between MSCs and the innate immune comaprtment are still unsolved. Here we describe an unconventional but functional interaction between pro-inflammatory classically activated macrophages (M1MФ) and MSCs, with CD54 playing a central role. CD54 was upregulated and enriched specifically at the contact area between M1MФ and MSCs. Moreover, the specific interaction induced calcium signaling and increased the immunosuppressive capacities of MSCs dependent on CD54 mediation. Our data demonstrate that MSCs can detect an inflammatory microenvironment via a direct and physical interaction with innate immune cells. This finding opens new perspectives for MSC-based cell therapy.

overall_design: Human bone-marrow derived mesenchymal stromal cells were co-cultivated with pro (M1MФ) or anti (M2MФ) -inflammatory macrophages. After 24h of co-culture, cells were detached and MSCs and MФ were magnetically separated based on the CD45 expression using the AutoMACS pro separator.

first: Nicolas

last: Espagnolle

first: Adélie

last: Balguerie

first: Emmanuelle

last: Arnaud

first: Luc

last: Sensebé


title: Expression of putative targets of immunotherapy in acute myeloid leukemia and healthy tissues.

status: Public on Jan 21 2017

city: Bethesda

first: Meghali

last: Goswami

state: MD

address: 10 Center Drive

department: Hematology

institute: NHLBI

summary: We analyzed using quantitative real-time PCR (qRT-PCR), gene expression of 65 potential leukemia associated antigens in de-identified, clinically annotated samples from ficoll purified peripheral blood samples from 22 newly diagnosed untreated AML patients collected under IRB-approved protocols from three NCCN cancer centers.

overall_design: qPCR gene expression profiling

first: Christopher

middle: S

last: Hourigan


title: Expression data from transfection of 14 different antisense oligonucleotides in HuH7 cells

status: Public on Apr 21 2017

city: Horsholm

first: Peter

middle: H

last: Hagedorn

state: Danmark

address: Fremtidsvej 3

department: Research

country: Denmark

institute: Roche Innovation Center Copenhagen A/S

summary: We used microarrays to globally profile the gene expression changes observed after 10h and 24h when transfecting antisense oligonucleotides in HuH7 cells

overall_design: 14 different antisense oligonucleotides (n=2 of each) were transfected into HuH7 cells and gene expression changes relative to mock-treated controls (n=2) were measured by microarray after 10h and 24h.


title: Expression data from transfection of an antisense oligonucleotide in 518A2 cells

summary: We used microarrays to globally profile the gene expression changes observed after 3 days when transfecting an antisense oligonucleotide in 518A2 cells

overall_design: An antisense oligonucleotides, denoted SPC2996 (n=3) was transfected into 518A2 cells and gene expression changes relative to mock-treated controls (n=3) were measured by microarray.


title: Single-cell molecular analysis defines therapy-response and immunophenotype of stem cell populations in CML

status: Public on Jan 27 2017

city: Lund

first: Mikael

middle: Nils Erik

last: Sommarin

state: skåne

address: klinikgatan 26, BMC B12

department: Department of molecular hematology

institute: Lund university

summary: Understanding leukemia heterogeneity is critical for the development of curative treatments as the failure to eliminate therapy-persistent leukemic stem cells (LSCs) may result in disease relapse. Here we have combined high-throughput immunophenotypic screens with large-scale single-cell gene expression analysis to define the heterogeneity within the LSC-population in chronic phase (CP) chronic myeloid leukemia (CML) patients at diagnosis and following conventional tyrosine kinase inhibitor (TKI) treatment. Our results reveal substantial heterogeneity within the putative LSC population in CP-CML and demonstrate differences in response to subsequent TKI-treatment between distinct subpopulations. Importantly, LSC subpopulations with myeloid and proliferative molecular signatures are proportionally reduced at a higher extent in response to TKI-therapy compared to subfractions displaying primitive and quiescent signatures. Additionally, cell surface expression of the CP-CML stem cell markers CD25, CD26 and IL1RAP is high on all subpopulation at diagnosis, but downregulated and unevenly distributed across subpopulations in response to TKI-treatment. The most TKI-insensitive cells of the LSC-compartment can be captured within the CD45RA- fraction and further defined as positive for CD26 in combination with an aberrant lack of cKIT expression. Thus, our results reveal the heterogeneity of the CML stem cell population and propose a Lin-CD34+CD38-/lowCD45RA-cKIT-CD26+ population to be targeted for improved therapy response.

overall_design: qPCR gene expression profiling of the HSC compartment of CML patients at diagnosis (Dx) and after TKI treatment (TKI). In total 29 96-well plates with pre-amplified HSC single-cell cDNA was loaded on to a 96.96 Dynamic Array Chip for Gene Expression. Sample IDs; nBM, Dx and TKI represents the clinical phase of patients, with nBM as a healthy control, Dx as the cells taken at diagnosis and finally TKI as the cells taken after 1-3 moths of TKI-treatment.

first: Rebecca

last: Warfvinge

first: Linda

last: Geironson Ulfsson

middle: N

first: Stefan

last: Lang

first: Shamit

last: Soneji

first: Göran

last: Karlsson


title: Intermittent calorie restriction largely counteracts the adverse health effects of a moderate-fat diet in aging C57BL/6J mice

status: Public on Jan 16 2017

first: Guido

last: Hooiveld

summary: Calorie restriction (CR) has been shown to extend life- and health-span in model species. For most humans, a life-long CR diet is too arduous to adhere to. The aim of this study was to explore whether weekly intermittent CR can 1) provide long-term beneficial effects and 2) counteract diet-induced obesity in male aging mice. In this study, we have exposed C57Bl/6J mice for 24 months to an intermittent (INT) diet, alternating weekly between CR of a control diet and ad libitum moderate-fat (MF) feeding. This weekly intermittent CR significantly counteracted the adverse effects of the MF diet on mortality, body weight and liver health markers in male 24-month-old mice. Hepatic gene expression profiles of INT-exposed animals appeared much more comparable to CR than to MF-exposed mice. At 12 months of age, a subgroup of MF-exposed mice was transferred to the INT diet. Gene expression profiles in the liver of the 24-month-old diet switch mice were highly similar to the INT-exposed mice. However, a small subset of genes was consistently changed by the MF diet during the first phase of life. Weekly intermittent CR largely, but not completely, reversed adverse effects caused by a MF diet.

overall_design: Male C57Bl/6J mice were divided to 3 dietary intervention groups: Control (AIN-93W), 30% calorie restriction (CR; AIN-93W-CR) and medium fat (MF; AIN-93W-MF; 25% energy from fat). Dietary interventions started at the age of 9 weeks and sacrifice was performed at the age of 6, 12, 24 and 28 months. We performed various measurements on metabolic parameters and gene expression analysis. This entry represents the microarray data. The array data from the 6-, 12- and 24-month-old mice exposed to the Control, CR and MF diet have been published before, and are also available under GEO accession number GSE84495.

first: Fenni

last: Rusli

first: Mark

last: Boekschoten

first: Miriam

last: van Dijk

first: Klaske

last: van Norren

first: Aswin

middle: L

last: Menke

first: Michael

last: Müller

first: Wilma

middle: T

last: Steegenga


title: High-sucrose/low-oil comparative genomic hybridization analysis in glycine max fast neutron mutants

status: Public on Jan 14 2017

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

summary: Two high-sucrose/low-oil mutants (FN0176450/2012CM7F040P06/SRX826343 and FN0176450/2012CM7F040P05/SRX826351) were identified in a soybean fast neutron population (Bolon et al. 2014). These mutant lines were then advanced to the M3:7 generation and compared to thier wild-type parent (M92-220-Long) using CGH to identify the causative region/gene associated with high-sucrose/low-oil.

overall_design: Four samples were analyzed, two plants from CM7F040P05 and two plants from CM7F040P06 fast neutron lines. Each sample was compared to its wild type parent (M92-220-Long) using Agilent CGH arrays.

first: Austin

last: Dobbels

first: Jean-Michel

last: Michno

first: Adrian

last: Stec


title: Spontaneous single-copy loss of TP53 in human embryonic stem cells markedly increases cell proliferation and survival [BeadChip]

status: Public on Jan 20 2017

city: La Jolla

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: The potential safety issues related to the acquisition of common genomic aberrations in hPSC cultures are well-recognized, but these risks have not been evaluated for sporadic mutations. Here, we explore whether a sporadic mutation that spontaneously arose in a hESC culture consisting of a single-copy deletion of chr17p13.1 would confer a survival advantage to the mutant cells. Compared to wild-type cells with two normal copies of the chr17p13.1 region, the mutant cells displayed a selective advantage when exposed to stressful conditions, and retained a higher percentage of pluripotent cells after two weeks of in vitro differentiation. Knockdown of TP53, which is a gene encompassed by the deleted region, in wild-type cells mimicked the chr17p13.1 deletion phenotype. RNA sequencing analysis showed differential expression of genes in pathways related to proliferation and differentiation. Thus, phenotypic implications of sporadic mutations must be taken into consideration before using the hPSC for clinical applications.

overall_design: 4 samples, two mutant WA09 lines with a single-copy deletion of chr17p13.1, and two wild-type WA09 lines were genotyped using the Illumina Omni5, which interrogates 4.3 million SNPs across the human genome.

first: Hadar

last: Amir

first: Louise

middle: C

last: Laurent


title: Temperature-dependent regulation of gene expression in Japanese flounder Paralichthys olivaceus treated with Edwardsiella tarda formalin-killed cells (FKC)

status: Public on Jan 15 2017

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

country: Japan

institute: Tokyo University of Marine Science and Technology

summary: 156 genes showed more than 4-fold up or down-regulated expressions by FKC at 15 ºC and 22 ºC.

overall_design: Fish were treated with FKC and reared at 15 ºC and 22 ºC and isolation of total RNA from spleen of the fish at 6 hours, 3days and 28 days after the treatment.

first: Norie

last: Kaneshige

first: Ikuo

last: Hirono


title: Transcriptome response of the Streptococcus pneumoniae D39 wild-type to N-acetyleglucosamine (NAG)

status: Public on Jan 12 2017

first: Sulman

last: Shafeeq

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown at in CDM with 0.5% Glucose to grown in CDM with 0.5 % N-acetyleglucosamine (NAG)

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

first: Muhammad

last: Afzal

first: Oscar

last: Kuipers


title: PIE cell line: Control vs. Poly(I:C) treated or Immunobiotic treated

status: Public on Jan 07 2017

city: San Miguel de Tucumán

first: Julio

last: Villena

state: Tucumán

address: Chacabuco 145

country: Argentina

institute: CERELA-CONICET

summary: We investigated the transcriptome response of porcine intestinal epitheliocyte cell line (PIE cells) to the challenge with the Toll-like receptor 3 (TLR3) agonist poly(I:C) and, the changes induced by immunobiotic Lactobacillus rhamnosus CRL1505 (Lr1505) or Lactobacillus plantarum CRL1505 (Lp1506) in that response. The transcriptome approach allowed us to obtain a global overview of the immune and immune related genes involved in response of PIE cells to the viral pathogen-associated molecular pattern poly(I:C). The most remarkable changes in PIE cells after Poly(:IC) challenge were observed in type I interferons and, interferon-induced genes, cytokines and chemokines expressions, followed by cell adhesion molecules and, prostaglandins. Previous work demonstrated in vitro and in vivo the capacity of both Lr1505 and Lp1506 to improve antiviral immunity. Here, we also confirmed that both immunobiotic lactobacilli differently modulates gene expression in poly(I:C)-challenged PIE cells. The microarray gene expression profiles demonstrated that Lr1505 and Lp1506 increased the expression of type I interferons as well as the antiviral factors MX1, MX2, OAS1, OASL, RNASE4 and RNASEL. In addition, lactobacilli were able to significantly improve the expression of cytokines (IL-1β, IL-6), chemokines (AMCF-II, CCL20, CCL28, CCL4, CXCL10, CXCL11) and, adhesion molecules (SEL-E, SEL-L, EPCAM, ICAM-1). Of interest, both Lr1505 and Lp1506 differentially modulated the expression of several genes related to prostaglandins including PTGS2, PTGIR, PTGES and, PTGFRN. The results show the ability of Lr1505 and Lp1506 to increase cellular factors involved in innate antiviral immunity that would explain their capacity to increase resistance to viral challenges observed in animal models. In addition, Lr1505 and Lp1506 may potentiate antiviral immunity by promoting the recruitment and activation of immune cells via the factors produced by the epithelial cells. The comprehensive analysis of gene expression in PIE cells by microarray allowed an important advance in the understanding of the mechanisms of action involved in the antiviral effect of immunobiotic lactobacilli.

overall_design: PIE cells were cultured for 3 days, L. rhamnosus CRL1505 or L. plantarum CRL1506 were added to cell cultures and 48 hours later cells were washed to eliminate bacteria. Non-bacteria treated PIE cells were used as controls. Then, cells were stimulated with Poly(I:C)  for 12 hours for microarray studies. Groups: unchallenged PIE cells, PIE cells + Poly(I:C), PIE cells + Lr1505 + Poly(I:C), PIE cells + Lp1506 + Poly(I:C). One replicate for each group.

first: L

last: Albarracin

first: H

last: Kobayashi

last: Kitazawa

first: J


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

status: Public on Jan 17 2017

summary: Transcriptome Comparison of the Streptococcus pneumoniae D39 wild-type grown in CDM with 0.03 mM to 50mM Cysteine


title: Investigation of molecular events underlying the IL-6-mediated Th1 inhibition in tumor-bearing mice

status: Public on Jan 04 2017

city: Kyoto

first: Hirotake

last: Tsukamoto

state: Sakyo-Ku

address: 53 Kawahara-cho Shogoin

department: Center for Cancer Immunotherapy and Immunobiology

institute: Kyoto University

summary: To understand the molecular mechanism underlying the IL-6-mediated attenuation of Th1 differentiation in tumor-bearing animals, we have employed whole genome microarray expression profiling of CD4+ T cells isolated from tumor-bearing mice. In order to distingish the effect of IL-6/sIL-6R signaling augmented in tumor-bearing mice from the effecct of other tumor-derived signals, we isolated CD4+ T cells that were primed in tumor free-mice and in the mice inoculated with ovalbumin (OVA)-expressing MCA205 fibrosamcoma, in conjunction of anti-IL-6R Ab injection. We found that Th2-like gene signature such as Il4, IL10, Ccr4, and c-maf was up-regulated in CD4+ T cells primed in tumor-bearing mice. However,the expression of other Th2 master regulator Gata3 gene, or Tfh-related genes (Bcl6, Cxcr5, and Batf) was not substantially augmented in tumor-bearing mice as compared with those in tumor-free mice. These expressions were abrogated by IL-6R blockade, suggesting that the expression of these Th2-like gene set and the other IL-6 signal-dependent genes like Klf1, Bcl11a, and Klf4 are candidate regulators responsible for IL-6 signaling-mediated Th1 inhibition in tumor-bearing animals.

overall_design: The differential gene expressions in CD4+ T cells primed in tumor-free vs MCA205-OVA-bearing mice, and in control Ab-treated vs anti-IL-6R Ab-treated MCA-OVA tumor-bearing mice were measured.  Two independent experiments were performed in each condition.

first: Koji

last: Fujieda


title: Insights into the ecology and evolution of the mucus-dwelling gut bacterium Mucispirillum schaedleri

status: Public on Jan 09 2017

first: Guido

last: Hooiveld

summary: Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals. To gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and tested for traits predicted by the genome using physiological experiments. Although thought to be a mucus degrader, its genome surprisingly predicts that M. schaedleri has limited capacity for degrading host-derived mucosal glycans or other complex polysaccharides. Rather, it may utilize small compounds such as peptides, amino acids, glycerol, and short chain fatty acids. Additionally, it can reduce nitrate and has systems for scavenging oxygen and reactive oxygen species, which accounts for its presence close to the mucosal tissue and during inflammation. Also of note, M. schaedleri harbors a type VI secretion system (T6SS) and several putative effector proteins containing eukaryotic domains, which suggest intimate interactions with the host and a role in inflammation. Examination of the individual phylogenies of all genes in the M. schaedleri genome revealed extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria. Though M. schaedleri utilizes non-horizontally-transferred pathways (e.g. nitrate reduction), horizontally-acquired pathways from gut organisms (e.g. T6SS and glycerol-P utilization) are also likely also important for its survival in the intestine, suggesting that lateral gene transfer may have played a key role in facilitating its establishment in the gut ecosystem.

overall_design: C57BL/6 mice harboring a reduced Altered Schaedler flora (ASF4; n=6) or ASF4 mice colonized with M. schaedleri MCS for 10 days (n=6) were sacrificed, whereafter cecum tissue was sbjected to gene expression profiling.

first: D

last: Berry

first: C

last: Pfann

first: M

last: Steinberger

first: B

last: Hanson

first: S

last: Herp

last: Brugiroux

last: Gomes Neto

last: Boekschoten

last: Schwab

first: T

last: Urich

first: A

last: Ramer-Tait

last: Rattei

last: Stecher

last: Loy


title: Real-time quantitative PCR array analysis of primary colon cancer and liver metastasis derived exosomes

city: Louisville

first: Huang-Ge

last: Zhang

state: KY

address: 505 S Hancock Street

department: James Graham Brown Cancer Center

institute: University of Louisville

summary: To isolate exosomes from colon tissue, colon tissue were removed and gently disaggregated with tweezers in dissociation buffer, followed by incubation at 37°C for 1 h. The disaggregated samples were centrifuged at 1,000 g for 10 min, 2,000 g for 20 min, 4,000 g for 30 min and 10,000 g for 1 h with the supernatant being retained each time. The tissue exosomes were collected by centrifuging the samples at 100,000 g for 1.5 h at 4°C, and the pellet was suspended in ice-cold PBS. Total RNA was isolated from cells, exosomes and tissue using a miRNeasy mini kit (Qiagen). miRNA expression profiling including exosomes and their donor cells or tissues was performed using the Qiagen miScript miRNA PCR Array Mouse miRBase Profiler.  To isolate exosomes from liver tissue, a 20-G catheter was inserted into the portal vein of anaesthetized mice. The perfused liver tissue, as well as colon tissue were removed and gently disaggregated with tweezers in dissociation buffer, followed by incubation at 37°C for 1 h. The disaggregated samples were centrifuged at 1,000 g for 10 min, 2,000 g for 20 min, 4,000 g for 30 min and 10,000 g for 1 h with the supernatant being retained each time. The tissue exosomes were collected by centrifuging the samples at 100,000 g for 1.5 h at 4°C, and the pellet was suspended in ice-cold PBS. Total RNA was isolated from cells, exosomes and tissue using a miRNeasy mini kit (Qiagen). miRNA expression profiling including exosomes and their donor cells or tissues was performed using the Qiagen miScript miRNA PCR Array Mouse miRBase Profiler.

overall_design: qPCR miRNAs expression profiling. One million CT26 colon cancer cells were administered into intra splenic injection or colonic submucosa via endoscopic work station. On day 3, 7, and 14 mice were sacrificed and tumors were removed and miRNA expression profiling including exosomes and their donor cells or tissues was performed using the Qiagen miScript miRNA PCR Array.

first: Teng

last: Yun


title: Gene expression profiles in several organs after treatment of rodents with Complex I inhibitors

status: Public on Jan 02 2017

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

country: Germany

institute: Bayer Pharma AG

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

overall_design: Refer to individual Series


title: Impact of ccpA delation on the transcriptome of Streptococcus pneumoniae D39 in the presece of N-acetylglucosamine (NAG)

first: Sulman

last: Shafeeq

summary: Transcriptome comparision of the Streptococcus pneumoniae D39 ccpA mutant to D39 wild-type grown in CDM + 0.5 % N-acetylglucosamine (NAG)

overall_design: One condition design comparision of two strains including a dye swap

first: Muhammad

last: Afzal

first: Oscar

last: Kuipers


title: Expression data from brain stem of rats with and without rotenone treatment

summary: We investigated an subacute study in male Wistar rats, treated daily with 400 ppm rotenone for 1, 3, or 14 consecutive days, followed by necropsy 24h after the last application. Rotenone is a strong mitochondrial respiratory chain complex I inhibitor. Inhibitors of complex I are suggested to exert anti-tumor activity of those tumors relying on oxidative metabolism and are therefore of interest in oncology research. Nevertheless, the safety profile of these inhibitors needs to be rigorously assessed. Rotenone has shown anti-carcinogenic activity in several studies. In this context we used rotenone in our study as tool compound with the aim to identify suitable biomarker candidates and enhance mechanistic insights into the biologic and cellular effects of complex I inhibitors at the organ level after in vivo treatment. Various parameters, including hematology, clinical chemistry and histopathology, major blood cell population phenotyping using FACS and enzymatic activity assays were measured and/or evaluated. Moreover gene expression profiles were determined to investigate pathways and functions affected by rotenone at the molecular level. As organs, liver, heart and brain stem were chosen due to the high metabolic activity, the high energy demand and due to the known neurotoxic effect of rotenone, respectively. The strongest rotenone-induced effects on gene expression were observed in the liver (1444 deregulated genes) compared to heart (650 deregulated genes) and brain stem (52 deregulated genes). These findings, together with the histopathological results, show that liver is a target organ of rotenone.

overall_design: Male RccHan Wistar rats at the age of 7-8 weeks were randomly assigned to the vehicle or treatment group (n=5). Then 0 or 400 ppm rotenone (Sigma Aldrich, Steinheim, Germany) was administered in the diet for 1, 3 or 14 consecutive days, followed by necropsy. Blood was collected for clinical chemistry and hematology and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation.

first: Sabrina

last: Heinz


title: Mouse iPSC: shNT versus shCtip

status: Public on Jan 10 2017

city: Sevilla

first: Daniel

last: Gomez-Cabello

state: Sevilla

address: Americo Vespucio

country: Spain

institute: CABIMER

summary: Copy variation number of iPSCs reprogrammed in presence (shNT) or abscence of Ctip protein (shCtip). This study shows genetic variations generated by CtIP abscence during Reprogramming process.

overall_design: 2 biological clones obtained of several pool reprogramming procedures. Clones were validated for Ctip expression.

last: Gómez-Cabello

first: Cintia

last: Checa-Rodríguez

first: María

last: Abad

first: Manuel

last: Serrano

first: Pablo

last: Huertas


title: Functional analysis of the zebrafish glucocorticoid receptor beta-isoform

status: Public on Jan 01 2017

city: Leiden

first: Marcel

last: Schaaf

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

summary: In the present study, we have used the zebrafish to investigate the functional role of the glucocorticoid receptor beta-isoform (GRbeta). A transgenic zebrafish line, Tg(hsp70:Gal4, UAS:EGFP-grbeta), was generated, showing heat shock-inducible expression of a GFP-tagged GRbeta. After heat shock treatment at 1 and 2 days post fertilization (dpf), 3 dpf larvae (control and transgenic) were treated with beclomethasone. A microarray study was performed to study transcriptional effects of GRbeta: its effect on transcription in the absence of beclomethasone (intrinsic transcriptional activity) and its effects on beclomethasone-induced transcriptional changes (dominant-negative activity). Although the microarray results revealed minor transcriptional effects of GRbeta expression, these data could not be validated using qPCR. It was therefore concluded that GRbeta did not show any transcriptional activity under these conditions.

overall_design: This microarray study was designed to determine the transcriptional effect of the glucocorticoid receptor beta-isoform. For this purpose, a transgenic zebrafish line, Tg(hsp70:Gal4, UAS:EGFP-grbeta), was generated showing heat shock-inducible expression of a GFP-tagged GRbeta. Control (wild type) and transgenic embryos were heat-shocked (2.5 hours at 37°C) at 1 and 2 dpf. At 3 dpf, larvae were treated with vehicle or beclomethasone (25 microM) for six hours. This resulted in 4 treament groups: con/veh, con/beclo, GRbeta/veh, GRbeta/beclo. RNA was isolated from 20 larvae per treatment group. Four individual experiments were performed, and the resulting quadruplicate samples were analyzed by microarray, using a common reference approach.

last: Chatzopoulou

first: P

last: Schoonheim

first: V

last: Torraca

last: Meijer

first: H

last: Spaink

first: M


title: Expression data from livers of rats with and without rotenone treatment

last: Ellinger-Ziegelbauer


title: R. sphaeroides pBBBRUpsMx2 vs. R. sphaeroides pBBR under singlet oxygen stress

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

summary: Transcriptional profiling of R. sphaeroides pBBRUpsMx2 compared to control R. sphaeroides pBBR under high oxygen and singlet oxygen conditions.

overall_design: RNA samples collected from R. sphaeroides cells were analyzed by two-color microarrays

first: Lennart

last: Weber


title: Expression data from hearts (lest ventricle apex) of rats with and without rotenone treatment

first: Heidrun


title: Characterization of a potential ABC-type bacteriocin exporter protein from Treponema denticola

city: Chiyoda-ku

first: Kazuyuki

last: Ishihara

state: Tokyo

address: Misakicho 2-1-14

department: Microbiolgy

institute: Tokyo Dental College

summary:
Background: Treponema denticola is strongly associated with the development of periodontal disease.  Both synergistic and antagonistic effects are observed among bacterial species in the process of biofilm formation.  Bacteriocin-related genes have not yet been fully characterized in periodontopathic bacteria.  The aim of this study was to detect and characterize bacteriocin-associated proteins in T. denticola.
Methods: The whole genome sequence of T. denticola ATCC 35405 was screened with a Streptococcus mutans bacteriocin immunity protein (ImmA/Bip) sequence.  The prevalence of homologous genes in T. denticola strains was then investigated by Southern blotting.  Expression of the genes was evaluated by qRT-PCR.
Results: In the genome sequence of T. denticola, an amino acid sequence coded by open reading frame TDE_0719 showed 26% identity with the S. mutans ImmA.  Furthermore, two protein sequences coded by TDE_0425 and TDE_2431 in T. denticola ATCC 35405 showed ~40% identity with that coded by TDE0719.  Therefore, TDE_0425, TDE_0719, and TDE_2431 were designated as tepA1, A2, and A3, respectively.  Open reading frames showing similarity to the HlyD family of secretion proteins were detected downstream of tepA1, A2, and A3.  They were designated as tepB1, B2, and B3, respectively.  A gene harboring a bacteriocin-like signal sequence was detected upstream of tepA1.  The prevalence of tepA1 and A2 differed among Treponema species.  Susceptibility to chloramphenicol and ofloxiacin was slightly decreased in a tepA2 mutant while that to kanamycin was increased.  Expression of tepA3-B3 was increased in the tepA2 mutant.
Conclusion: These results indicate that T. denticola ATCC 35405 has three potential bacteriocin export proteins and that the presence of these genes differs among the Treponema strains.  These proteins may be involved in resistance to chloramphenicol.

overall_design: Comparison of 2 strains.  Wild type: Treponema denticola ATCC 35405, 1 sample.  Mutant: Treponema denticola TDE_0719 mutant, 1 sample.  All strains were harvested in early log phase.

first: Kimiko

last: Tanaka-Kumazawa

first: Yuichiro

last: Kikuchi

first: Yumiko

last: Sano-Kokubun

first: Seikou

last: Shintani

first: Masashi

last: Yakushiji

first: Howard

middle: K

last: Kuramitsu


title: Immunophenotypic and detailed cytogenetic characterization of cell lines derived from myelodysplastic syndrome patients after progression to acute myeloid leukemia

city: Badalona

first: Mar

last: Mallo

address: Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC

institute: Josep Carreras Leukaemia Research Institute

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

summary:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cultured cells.
Five cell lines (MOLM-13, SKM-1, F-36P, SKK-1 and OHN-GM) derived from myelodysplastic syndrome patients after progression to acute myeloid leukemia have been studied by flow cytometry, conventional cytogenetics and whole genome single nucleotide polymorphism microarrays, in order to deeply characterize.

overall_design: SNP-A (Cytoscan 750K) from 5 cell lines

first: Anna

last: Palau

first: Francesc

last: Solé

first: Marcus

last: Buschbeck


title: Rhodobacter sphaeroides 2.4.1 pRKSorX144 versus pRK415 under singlet oxygen stress.

summary: To learn more about the function of SorX, we constructed an over-expression strain. For this purpose, the sorX gene together with its 28-bp upstream region was cloned into the over-expression vector pRK4352 and expressed in the R. sphaeroides wild-type 2.4.1 background. The corresponding strain consequently exhibits a SorX over-expression that is driven by the constitutive 16S rRNA (RSP_4352) promoter. The over-expression strain was compared to an empty vector control (pRK415). Total RNA from the over-expression (pRKSorX144) and from the empty vector control (pRK415) strain was extracted after 7 min of singlet oxygen stress and used for microarray analysis to investigate SorX-induced changes on transcriptome level.

overall_design: RNA samples collected after 7 min of singlet oxygen stress were analyzed by two-color microarrays. Each microarray contains a pool of three independent biological replicates for each sample.

first: Tao

last: Peng

first: Bork

last: Berghoff


title: Effect of Glycyrrhetinic acid and its derivatives on antibacterial activity and virulence against Staphylococcus aureus

city: Kagoshima City

first: Kentaro

last: Oyama

address: Sakuragaoka 8-35-1

institute: Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan

summary: To clarify the mechanism for the antibacterial activity of GR-SU, we performed the DNA microarray analysis.

overall_design: Gene expression in Staphylococcus aureus was measured at 2 hours after exposure to 128μg/ml of GR-SU.  Four independent experiments were performed using different samples for each experiment.

last: Ohyama

first: Miki

last: Kawada-Matsuo

first: Shingo

last: Ikeuchi

first: Yuichi

last: Oogai

first: Tatsuya

last: Nakahara

first: Tetsuya

last: Hayashi

first: Norifumi

last: Nakamura

first: Hitoshi

last: Komatsuzawa


title: Knock down effect of Ror2 on gene expression profiling in human osteosarcoma cells (SaOS2)

city: Wako

first: Kota

last: Tamada

state: Saitama

address: Hirosawa 2-1

department: BSI

institute: RIKEN

summary: Ror2 is a member of the Ror-family of receptor tyrosine kinases acting as a receptor for Wnt5a. Wnt5a/Ror2 signaling activates primarily the ß-catenin-independent pathway, which involves various signal mediators, such as Dishevelled, c-Jun N-terminal kinase (JNK), filamin A, c-Src, and Ca2+. Wnt5a/Ror2 signaling has also been shown to inhibit the ß-catenin-dependent pathway. Wnt5a and Ror2 are overexpressed in various types of tumor cells, including osteosarcoma and melanoma cells, resulting in constitutive activation of Wnt5a/Ror2 signaling in a cell-autonomous manner. Constitutively activated Wnt5a/Ror2 signaling has been shown to play important roles in promoting invadopodia formation and invasiveness of tumor cells. However, little is known about the mechanisms underlying these processes. As an attempt to understand the mechanism by which Wnt5a/Ror2 signaling, activated constitutively in osteosarcoma cells, contributes to their highly invasive properties, we performed DNA microarray analysis using a human osteosarcoma cell line, SaOS2.

overall_design: Human osteosarcoma cells (SaOS2) have been transfected with control (siCTL) or ROR2 (siROR2)-directed siRNA. Two biological replicate were used for the comparison of siCTL v.s. siROR2.

first: Michiru

last: Nishita

first: Masahiro

last: Enomoto

first: Toru

last: Takumi

first: Yasuhiro

last: Minami


title: Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

institute: University of Amsterdam

summary:
Study of transcriptome dynamics using a high-resolution gene-expression time course with 180 individual embryos, obtained from nine different spawns that are profiled from late blastula to mid gastrula stage.
All individual embryos of genotype ABTL were photographed and an initial developmental time was estimated using percentage epiboly as a metric.

overall_design: In this study development was studied at the level of the individual embryo and no treatment was applied.

first: Timo

last: Breit

first: Johanna

middle: F

last: Pagano


title: Role of an extracytoplasmic function sigma factor, PGN_0319, in hemin utilization by Porphyromonas gingivalis

first: Kazuyuki

last: Ishihara

summary: Extracytoplasmic function (ECF) sigma factors are known to play an important role in the bacterial response to various environmental stresses. Porphyromonas gingivalis, a prominent etiological agent in human periodontitis, possesses six putative ECF sigma factors. So far, information is limited on an ECF sigma factor, PGN_0319. It has been recently reported that the expression of genes encoding some of the ECF sigma factors including PGN_0319 was affected by hemin availability. The aim of this study was to evaluate the role of PGN_0319 in hemin utilization by P. gingivalis. We evaluated the gene expression profile of the PGN_0319 mutant by DNA microarray, and then real-time reverse transcription PCR analysis was performed to assess genes with altered expression levels. The expressions level of hmuY and hmuR, which encode an outer-membrane protein involved in hemin utilization, and cdhR, a transcriptional regulator of hmuYR, were significantly decreased in the PGN_0319 mutant. The transcription of these genes was restored in the PGN_0319 complemented strain. We observed that the PGN_0319 mutant showed reduced growth in log phase compared with wild type under hemin-limiting condition. By electrophoretic mobility shift assay we demonstrated the recombinant PGN_0319 protein bound to the promoter region of hmuY and cdhR. In addition, we observed that PGN_0319 gene was upregulated in response to low cell density. These results demonstrate that PGN_0319 play an important role in the early growth of P. gingivalis, and directly regulates hmuYR and cdhR, thereby plays a role in the mechanisms involved in hemin utilization by P. gingivalis.

overall_design: Comparison of 2 strains  Wild type: Porphyromonas gingivalis ATCC 33277, 2 samples  Mutant: Porphyromonas gingivalis PGN_0319 mutant, 2 samples  All strains were harvested in mid log phase.

first: Koki

last: Ota

first: Yuichiro

last: Kikuchi

last: Imamura

first: Daichi

last: Kita

first: Kouki

last: Yoshikawa

first: Atsushi

last: Saito


title: 20% (w/v) Glucose osmotic stress (YP20) vs 1M Sorbitol osmotic stress (YPS) in a hot1delta mutant

city: Burjassot (Valencia)

first: Marcel·lí

last: del Olmo

address: Dr Moliner, 50

department: Bioquímica i Biologia Molecular

institute: Universitat de València

summary:
Transcriptional profiling of yeast Saccharomyces serevisiae cells exposed to stress (30 min) compared to no stress conditions (YPD) in a hot1delta mutant
Two stress condition experiments, YP20 and YPS, each one compared to no-stress conditions (YPD) in a hot1delta mutant

overall_design: Two replicates of each condition

first: M

last: Gomar-Alba


title: Root-shoot mineral transport as a key target processes involved in Arabidopsis responsiveness to elevated [CO2] conditions

city: pamplona

first: Ivan

last: Jáuregui Mosquera

state: Navarra

address: Campus de Arrosadia, s/n,  Dpto. Ciencias del Medio Natural

institute: Universidad Pública de Navarra

summary:
In this study we explain the physiological, biochemical and gene expression mechanisms adopted by nitrate-fed Arabidopsis thaliana plants growing under elevated [CO2], highlighting the importance of root-to-shoot interactions in these responses
The transcriptomic approach (conducted at the root and shoot level) revealed that exposure to 800 ppm [CO2] conditioned the expression of genes involved in the transport of nitrate and mineral elements.

overall_design: Arabidopsis thaliana, Columbia 0 ecotype (col 0) plants grown under hydroponic conditions. The nitrogen (N) source was KNO3 at 0.75 mM concentration. 5 weeks exposure to CO2 treatments, previous to first flower were buds visible (see Supplemental Figure 1 for the image of the plants), in 3.9 growth stage ontology from the scale described by Boyes (2001).

first: Iván

last: Jáuregui

first: Pedro

last: Aparicio-Tejo

first: Concepción

last: Avila

first: Rafael

last: Cañas

first: Sandra

last: Sakalauskiene

first: Iker

last: Aranjuelo


title: Bioinformatic evaluation and comparison of parallel aSNP and aCGH analyses of myelodysplastic syndromes patients with normal karyotype

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

type: Genome variation profiling by genome tiling array

summary:
Parallel aSNP and aCGH analyses were performed on 22 samples from MDS patients with a normal karyotype. 55 overlapping alterations, most of these corresponding to CNVs were identified with both methods. Putative tumour specific imbalances were found with both methods in three cases, a deletion of TET2, a larger deletion containing DNMT3A and one complex molecular karyotype. In two cases putative tumour specific imbalances were only seen with aCGH: a 16p deletion in a low number of cells and a small homozygous deletion in WWOX. Telomeric UPDs were only detected with aSNP in two cases: one affecting chromosome 3q and in the other, two UPD regions were present on 4q and 5p. In total, putative relevant tumour specific genomic alterations were found in seven cases (32%). Three small aberrations only detected by aCGH were present in T-cells, suggestive of germ line alterations which may confer a risk for MDS development.
This part contains the aCGH analyses, for aSNP see GSE49004.

overall_design: Array CGH experiment, 22 MDS tumor cells and 5 blood cells vs. control DNA.

first: Sabrina

last: Claßen-von Spee

first: Mar

last: Mallo

first: Manfred

last: Beier

first: Simone

last: de Leve

first: Leonor

last: Arenillas

first: Carmen

last: Pedro

first: Francesc

last: Solé


title: Transcription profiling of A. thaliana L.er vs fe-1

city: Bunkyo-ku

first: Mitsutomo

last: Abe

address: 7-3-1 Hongo

department: Department of Biology

institute: The University of Tokyo

summary:
The Arabidopsis thaliana Myb transcription factor, FE, acts as a key regulator of phase transition. In order to identify potential target genes of FE protein, we performed microarray experiments. Using fe-1 and transgenic plants overexpressing GR-tagged FE (35S::FE-GR), we compared transcriptional profiling of WT (L.er) vs fe-1 and Dex-treated 35S::FE-GR vs Mock-treated 35S::FE-GR.
Transcriptional profiling of A. thaliana comparing WT (L.er) with the fe-1 mutant

overall_design: WT (L.er) vs fe-1: 2 biological replicates. Dex vs Mock treatment of 35S::FE-GR (#5)

first: Ayako

last: Yamaguchi


title: Characterization of CD1- and CD1+ porcine blood dendritic cells confirm them as orthologues of the two major mammalian conventional subsets

status: Public on Dec 31 2016

city: Addlestone

first: Helen

middle: Elizabeth

last: Everett

state: Surrey

address: New Haw

department: Virology

country: United Kingdom

institute: Animal and Plant Health Agency (APHA)

summary: Porcine CD1- and CD1+ dendritic cells represent the orthologues of human and mouse cDC1 and cDC2 cellssubsets respectively

overall_design: Porcine CD1- and CD1+ dendritic cells

first: Simon

last: Graham

first: Jane

last: Edwards

first: Falko

last: Steinbach


title: Arabidopsis Col and nore1-1 at DAE 12, 16, 20, and 24

status: Public on Sep 14 2016

city: Jeju-si

first: Jeongsik

last: Kim

state: Jeju

address: 102 Jejudaehakroe

department: Faculty of Science Education

country: South Korea

institute: Jeju National University

summary: To understand the role of NORE1, a negative regulator of senescence during senescence, we have employed transcriptional profiling of Col and nore1-1 along aging (DAE 12,16,20 and 24). Aligent’s Whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Age (4 time points; DAE12, 16, 20, and 24)-associated transcription profile in Col vs nore1-1. 2 independent biological samples

first: Il Hwan

last: Lee

first: Jeonsik

first: Hye Ryun

last: Woo


title: The methylome of murine foetal skin and scarless wound healing

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

department: Molecular Biotechnology and Microbiology

country: Poland

institute: Gdansk University of Technology

type: Methylation profiling by genome tiling array

summary: Foetal skin is known to heal without scar. This ability is lost in the third trimester of gestation. In mouse, scarless wound healing was reported until the day 15-16 of gestation. A range of factors that could explain the mechanisms of scarless skin wound healing have been identified, to mention reduced immune response, a greater proportion of collagen type III, hyaluronic acid and transforming growth factor beta isoform 3.  The involvement of epigenetic changes, which are known to determine developmental processes, has not been examined in the context of scarless foetal skin healing so far.   We performed the microarray analysis methylome and transcriptome of murine foetal dorsal skin at embryonic day 15 contrasted with those in later phases at embryonic days 18-19 as well as the in the adult mouse. The group of genes which show decreased methylation status in the foetal skin before the loss of ability to scarless healing between embryonic day 15 and 18 are enriched with transcriptional factors involved in embryonic morphogenesis, epithelium development, neuron differentiation, and synapse functions. The genes with increased methylation after the transition are associated with cell death and epithelial cell differentiation, inflammatory and wounding response and the degradation of hyaluronic acid. A substantial part of DNA methylation differences observed between embryonic day 15 and 18 were retained later at embryonic day 19 and in adults and remarkably correlated with gene expression changes. A major part of genes encoding the key factors responsible for cutaneous wound healing show significant changes in gene expression following  the transition  from scar free to normal healing.    The results show that skin methylome and transcriptome undergoe extensive alterations following the loss of ability to scarless healing, while the functions associated with the changes imply their central role in skin wound repair.

overall_design: genome-wide DNA methylation profiling in the dorsla skin tissue at different stages of development of the C57BL/6J mouse strain

first: Paweł


title: Characterization of tumor-associated-macrophage of breast cancer patient-derived xenografts

status: Public on Oct 11 2016

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
The aim of this study was to characterize the stroma displayed by different models of breast cancer tumors in mice. For this purpose, transcriptomic and flow cytometry analyses on murine populations were performed in a series of 25 PDXs and 2 most commonly used GEMs (MMTV-PyMT and MMTV-erBb2). Specifically, macrophages from 5 models were sorted and profiled by gene expression and phenotypically characterized by flow cytometry.
Composition of hematopoietic cells, mainly macrophages and granulocytes, varied tumor from tumor. Macrophages were shown to display specific polarization phenotype related to M1/M2 classification and associated with genes implicated in recruitment, invasion and metastasis processes. The heterogeneity of stroma component of the studied models suggests that tumor cells educate their microenvironment to fulfill their needs. This observation therefore supports the relevance of such models for preclinical study purposes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Macrophage/monocyte-like cells (EpCAM-CD45+F4/80+) were sorted on a FACS

first: David

last: Vallerand

first: Gérald

last: Massonnet

first: Fatima

last: Kebir

last: Gentien

first: Zofia

last: Maciorowski

first: Brigitte

last: Sigal-Zafrani

first: Marion

last: Richardson

first: Sandrine

last: Humbert

first: Aurélie

last: Thuleau

first: Franck

last: Assayag

first: Ludmilla

last: Deplater

first: André

last: Nicolas

first: Suzy

last: Scholl

first: Elisabetta

last: Marangoni

first: Stefan

last: Weigand

first: Sergio

last: Roman-Roman

first: Ariel

last: Savina

first: Didier

last: Decaudin


title: The overexpression of the pine transcription factor PpDof5 in Arabidopsis leads to increased lignin content and affects carbon and nitrogen metabolism.

status: Public on Oct 01 2016

city: Málaga

first: Marina

last: Rueda López

state: Málaga

address: Campus Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

summary: Transcriptional profiling of Arabidopsis transgenic plants overexpresing PpDof5, a transcription factor of Pinus pinaster. Plants were grown with nitrate or ammonium as unique source of nitrogen

overall_design: Four-condition experiment: wt Arabidopsis vs. transgenic Arabidopsis plants overexpressing PpDof5 grown with nitrate or ammonium. 2 Biological replicates and 2 technical replicates.

last: Rueda-López

first: Rafael

last: Cañas

first: Javier

last: Canales

first: Francisco

last: Cánovas

first: Concepcion

last: Ávila


title: CNV in spruce

status: Public on Dec 14 2016

city: Quebec

first: Julien

last: Prunier

state: QC

address: 1030 av. de la medecine

department: Forestry

country: Canada

institute: Université Laval

summary:
We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays. Gene CNVs were assessed in three full-sib families from species with 20 Gb genomes, i.e. white and black spruce, and interior spruce - a natural hybrid.
Results: We discovered hundreds of gene CNVs in each species, 3612 in total, which were enriched in functions related to stress and defense responses and narrow expression profiles, indicating a potential role in adaptation. The number of shared CNVs was in accordance with the degree of relatedness between individuals and species. The genetically mapped subset of these genes showed a wide distribution across the genome, implying numerous structural variations. The hybrid family presented significantly fewer CNVs, suggesting that the admixture of two species within one genome reduces the occurrence of CNVs.

sample_organism:
Picea glauca
Picea mariana
Picea engelmannii x Picea glauca

overall_design: CNV analysis of descendent and parental White Spruce (Picea glauca), Interior Spruce (Picea engelmannii x Picea glauca) and Black Spruce (Picea mariana)

first: John

last: MacKay

first: Sébastien

last: Caron


title: Shewanella piezotolerans WP3 wild-type strain under high hydrostatic pressure

status: Public on Sep 10 2016

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

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

overall_design: Refer to individual Series


title: Methionine-mediated gene expression and characterization of the CmhR regulon in Streptococcus pneumoniae

status: Public on Oct 15 2016

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

institute: Karolinska Institutet

summary: In this study, we investigated the transcriptomic response of Streptococcus pneumoniae D39 to methionine. Transcriptome comparison of the S. pneumoniae D39 wild-type grown in chemically defined medium (CDM) with 0mM to 10mM methionine revealed the elevated expression of various genes/operons involved in methionine synthesis and transport (fhs, folD, gshT, metA, metB, metEF, metQ, tcyB, spd-0150, spd-0431, and spd-0618). We further demonstrated by β-galactosidase assays and quantitative RT-PCR studies that the transcriptional regulator, CmhR (SPD-0588) acts as a transcriptional activator of the fhs, folD, metB, metEF, metQ, and spd-0431 genes. We identified a putative regulatory site of CmhR in the promoter region of CmhR regulated genes and this CmhR site was further confirmed by promoter mutational experiments.

overall_design:
Comparison of the Streptococcus pneumoniae D39 wild-type grown in CDM with 10mM added methionine to D39 wild-type grown in CDM with 0mM added methionine.
Two conditions design comparison of one strain including a dye swap.

first: Muhammad

last: Afzal

first: Oscar

last: Kuipers


title: Pseudomonas putida KT2440 : Control vs. indole or ampicillin or indole plus ampicillin treated

city: Seoul

first: Jisun

last: Kim

address: Anam-Dong, Sungbuk-Gu

department: Environmental Science and Ecological Engineering

institute: Korea university

summary: Transcriptional profiling of P. putida KT2440 cells comparing untreated cells with 1 mM indole or 50 μg/ml ampicillin or 1 mM indole plus 50 μg/ml ampicillin treated cells

overall_design: Four-condition experiment, Control vs. 1 mM indole treatment,  Control vs. 50 μg/ml ampicillin treatment, Control vs. 1 mM indole and 50 μg/ml ampicillin treatment

first: Woojun

last: Park


title: Docosahexaenoyl Serotonin, an endogenously formed n-3 fatty acid-serotonin conjugate, has anti-inflammatory properties by attenuating IL23–IL17 signalling in macrophages.

status: Public on Sep 27 2016

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary:
Conjugates of fatty acids and amines, including endocannabinoids, are known to play important roles as endogenous signalling molecules. Among these, the ethanolamine conjugate of the n-3 poly unsaturated long chain fatty acid (PUFA) docosahexaenoic acid (22:6n-3) (DHA) was shown to possess strong anti-inflammatory properties.

Previously, we identified the serotonin conjugate of DHA, docosahexaenoyl serotonin (DHA-5-HT), in intestinal tissues and showed that its levels are markedly influenced by intake of n-3 PUFAs. However, its biological roles remain to be elucidated. Here, we show that DHA-5-HT possesses potent anti-inflammatory properties by attenuating the IL-23-IL-17 signalling cascade in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages. Transcriptome analysis revealed that DHA-5-HT down-regulates LPS-induced genes, particularly those involved in generating a CD4 + Th17 response. Hence, levels of PGE2, IL-6, IL-1β, and IL-23, all pivotal macrophage-produced mediators driving the activation of pathogenic Th17 cells in a concerted way, were found to be significantly suppressed by concentrations as low as 100–500 nM DHA-5-HT. Furthermore, DHA-5-HT inhibited the ability of RAW264.7 cells to migrate and downregulated chemokines like MCP-1, CCL-20, and gene-expression of CCL-22 and of several metalloproteinases. Gene set enrichment analysis (GSEA) suggested negative overlap with gene sets linked to inflammatory bowel disease (IBD) and positive overlap with gene sets related to the Nrf2 pathway. The specific formation of DHA-5-HT in the gut, combined with increasing data underlining the importance of the IL-23-IL-17 signalling pathway in the aetiology of many chronic inflammatory diseases merits further investigation into its potential as therapeutic compound in e.g. IBD or intestinal tumorigenesis.

overall_design: RAW264.7macrophages were stimulated with LPS (1 µg/ml) and incubated with 1 µM of DHA-5-HT or vehicle control for 24 h and subjected to microarray analysis.

first: Mieke

last: Poland

first: Jean

last: ten Klooster

first: Zheng

last: Wang

first: Raymond

last: Pieters

first: Mark

middle: V

last: Boekschoten

first: Renger

last: Witkamp

first: Jocelijn

last: Meijerink


title: Supplementation with Lactobacillus plantarum WCFS1 prevents Decline of Mucus Barrier in Colon of Accelerated Aging Ercc1-/Δ7 Mice

status: Public on Oct 19 2016

summary: Although it is clear that probiotics improve intestinal barrier function, little is known about the effects of probiotics on the aging intestine. We investigated effects of 10-wk bacterial supplementation of Lactobacillus plantarum WCFS1, Lactobacillus casei BL23, or Bifidobacterium breve DSM20213 on gut barrier and immunity in 16-week-old accelerated aging Ercc1-/Δ7 mice, which have a median lifespan of ~20wk, and their wild-type littermates. The colonic barrier in Ercc1-/Δ7 mice was characterized by a thin (<10µm) mucus layer. L. plantarum prevented this decline in mucus integrity in Ercc1-/Δ7 mice, whereas B. breve exacerbated it. Bacterial supplementations affected the expression of immune-related genes, including Toll-like receptor 4. Regulatory T cell frequencies were increased in the mesenteric lymph nodes of L. plantarum- and L. casei-treated Ercc1-/Δ7 mice. L. plantarum- and L. casei-treated Ercc1-/Δ7 mice showed increased specific antibody production in a T cell-dependent immune response in vivo. By contrast, the effects of bacterial supplementation on wild-type control mice were negligible. Thus, supplementation with L. plantarum – but not with L. casei and B. breve – prevented the decline in the mucus barrier in Ercc1-/Δ7 mice. Our data indicate that age is an important factor influencing beneficial or detrimental effects of candidate probiotics. These findings also highlight the need for caution in translating beneficial effects of probiotics observed in young animals or humans to the elderly.

overall_design: The effects of 10-wk bacterial supplementation of Lactobacillus plantarum WCFS1, Lactobacillus casei BL23, or Bifidobacterium breve DSM20213 on gut barrier and immunity was investigated in 16-week-old accelerated aging Ercc1-/Δ7 mice, which have a median lifespan of ~20wk, and their wild-type littermates.

first: Adriaan

last: van Beek

first: Bruno

last: Sovran

first: Floor

last: Hugenholtz

first: Ben

last: Meijer

first: Joanne

last: Hoogerland

first: Violeta

last: Mihailova

first: Corine

last: van der Ploeg

first: Clara

last: Belzer

first: Jan

last: Hoeijmakers

first: Wilbert

last: Vermeij

first: Paul

last: de Vos

first: Jerry

last: Wells

first: Pieter

last: Leenen

first: Claudio

last: Nicoletti

first: Rudi

middle: W

last: Hendriks

first: Huub

last: Savelkoul


title: Maternal exposure to a Western-style diet causes differences in microbiota composition and gene expression in the intestine of suckling mouse pups

status: Public on Aug 22 2016

first: Guido

last: Hooiveld

summary: During the last few decades, the long-lasting consequences of nutritional programming during the early phase of life have become increasingly evident, but the effects of maternal nutrition on the developing intestine are currently still relatively underexplored. In this study, we investigated in mice the effects of a maternal Western-style (WS) high fat/cholesterol diet, given during the perinatal period, on gene expression and microbiota composition of two-week-old offspring. Microarray analysis revealed that a perinatal WS diet caused significant changes in gene expression in the small intestine and colon of the suckling offspring. A strong sexually dimorphic effect was observed in the affected genes. However, pathway analysis of the differentially expressed genes displayed that in both sexes metabolic and immune functions were strongly affected. Integration of the microbiota and gene expression data applying a multivariate correlation analyses revealed that Bacteroidaceae, Porphyromonadaceae and Lachnospiraceae were the bacterial families that most strongly correlated with gene expression in the colon and not with the bacterial families displaying the most pronounced change due to perinatal exposure to a WS diet. Amongst the genes demonstrating a strong correlation with one or more bacterial families were genes of key importance for intestinal development or functioning (i.e., Pitx2 and Ace2). In conclusion, our data demonstrate a strong programming effect of a maternal WS diet on the development of the intestine in the offspring.

overall_design: Small intestine and colon were isolated from two-week-old pups of dams fed a low- or Western-style high fat/cholesterol diet and subjected to gene expression profiling.

first: Wilma

last: Steegenga

first: Mona

last: Mischke

first: Mark

last: Boekschoten

first: Carolien

last: Lute

first: Torsten

last: Plosch

first: Michael

last: Muller

middle: J


title: The transcriptome of murine foetal skin and scarless wound healing

first: Pawel

last: Sachadyn

overall_design: 5 samples, each sample is a pool representing three animals

first: Paweł


title: Shewanella piezotolerans WP3 wild-type strain under cold shock

first: Huahua

last: Jian


title: Analysis of BES1-PIF4 interdependency in gene expression

status: Public on Aug 05 2016

city: Madrid

first: Ana

last: Espinosa-Ruiz

state: Madrid

department: Centro Nacional de Biotecnología

institute: CSIC

summary: BES1 transcription factor is a master regulator of brassinosteroid signalling. Part of BES1 activity as a transcription factor is brought about upon dimerization with light-responsive PIF4 transcription factor. To analyse BES1-dependent transcriptional cascade, and to which extent BES1 requires PIF4/PIF5 for target gene regulation, we performed microarray analysis of the following phenotypes: Col-0, bes1-D, pif4pif5 and bes1-D;pif4pif5 in dark grown seedlings.

overall_design: Col-0, bes1-D, pif4pif5 and bes1-D;pif4pif5 5-days seedlings grown in the dark were used for RNA extraction. 3 independent biological samples were collected for each genoptye.

first: Salomé

last: Prat

first: Cristina

last: Martínez


title: Microarray expression profile analysis of long non-coding RNA in androgenetic alopecia: a study of Chinese men

status: Public on Jul 27 2016

city: Shenyang

first: Lin

middle: Lin

last: Bao

state: Liaoning

address: 155N. Nanjing Street, Heping district

department: Dermatology Department

institute: First Hospital of China Medical University

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

summary: To examined the genome-wide expression levels of lncRNAs in androgenetic alopecia tissues and paired adjacent normal tissues by microarray analysis. We identified numerous lncRNAs that were differentially regulated between androgenetic alopecia and paired normal tissues.

overall_design: Collected 3 pairs of male scalp androgenetic alopecia tissues and adjacent normal tissues, then extracted mRNAs from the tissues and transcripted the mRNAs into cRNAs. Then, cRNAs were hybridized onto the Human LncRNA Expression Microarrays. And then analyzed the results.

first: Yuanhong

last: li

first: Linlin

first: Aijiao

last: Yu

first: Xuegang

last: Xu


title: miRNA expression during differentiation of white and brown adipocytes

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

institute: Tsinghua University

summary: miRNA array of a timecourse of 3T3-L1 differentiating into white adipocytes and C3H10T1/2 into brown adipocytes

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 3T3-L1 cells were differentiated into white adipocytes, C3H10T1/2 were differentiated into brown adipocytes, and samples were havested at different timepoints of differentiation.

first: Reinhard

last: Brunmeir

first: Jingyi

last: Wu

first: Xu

last: Peng

first: Feng


title: Effects of age and exposure to cyclic ovarian hormones on mouse myometrium

status: Public on Jul 17 2016

city: Cambridge

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

institute: University of Cambridge

summary: Delaying first childbirth is associated with a range of pregnancy complications, but the mechanisms underlying this are unclear. We have hypothesized that prolonged, cyclical, pre-pregnancy exposure to estrogen and progesterone contributes to age-related deterioration of uterine function.  We conducted a series of studies in virgin mice of varying age and exposure to hormonal manipulations. We compared the myometrial transcript profile from young (10-12 weeks, n=7) and old (28-30 weeks, n=7) mice.  We validated this list using a second experiment of young versus old mice housed in a different animal facility and comparing animals of 10-12 (n=8) and 38-40 (n=7) weeks of age. The pattern of change in these transcripts was very similar.  We determined whether removal of the ovaries in early life (8-10 weeks of age) prevented age-related changes.  When we compared old animals (38-40 weeks) which had early ovariectomy (n=7) with sham operated controls of the same age (n=7), we found that the transcripts which had been down-regulated by age were upregulated in old animals that had an early ovariectomy.  The converse was observed for genes which had been downregulated by age.  Hence, early ovariectomy prevented changes in myometrial gene expression associated with aging.   We then studied the effect of prolonged, continuous exposure to progesterone between 8 and 36 weeks of age.  When we compared old animals (38-40 weeks) that received progesterone implants from 8 to 36-38 weeks (n=10) with old animals receiving implants containing only vehicle (n=5), transcripts which had been down-regulated by age were upregulated by prolonged exposure to progesterone.  The converse was observed for genes which had been downregulated by age.  Hence, prolonged exposure to progesterone also ameliorated changes in myometrial gene expression associated with aging.

overall_design: Mouse myometrium from young, old, control or treated groups. 5 to 10 replicates per group

first: D

middle: S

first: Gordon

last: Smith

first: Hsu

middle: P

last: Chong


title: Expression profile from Saccharomyces cerevisiae strains deleted for PMR1 treated with 5mM CaCl2

city: Sevilla

first: Ralf

middle: Erik

last: Wellinger

address: Avd Americo Vespucio SN

department: Molecular Biology

institute: CABIMER_Universidad de Sevilla

summary:
Pmr1 is a cis-Golgi Mn/Ca transporter with a key role in protein glycosylation and manganese detoxification.
We used microarray analysis to analyze the impact of CaCl2 supplementation on gene expression in pmr1∆ mutants and found that extracellular CaCl2 suppresses transcriptional misregulation in pmr∆ mutants.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: S. cerevisiae strains were grown in YPAD liquid culture  supplemented with 5mM CaCl2, total RNA was isolated and hybridized on Affymetrix microarrays.

first: Nestor

last: Garcia-Rodriguez


title: Transcript profiling of six rice cultivars with different tolerance level under high night temperatures

status: Public on Dec 01 2016

city: Potsdam-Golm

first: Ulrike

last: Glaubitz

address: Am Mühlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

summary: Regulation of transcript expression in different tolerance classes of rice cultivars in response to high night temperatures (HNT) is investigated. The aim was to identify marker genes which are responsible for HNT tolerance. Addiditionally gene expression data are combined with GC-MS data analysis (primary metabolites) to identify global changes in response to HNT.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: Six rice cultivars of both subspecies, indica and japonica, are analyzed. High night temperature (HNT) sensitivity is known and 2 cultivars of each class (tolerant, intermediate, sensitive) are investigated under two different conditions (control and HNT treatment). Three independent experiments of each condition were performed to gain 3 biological replicates for each cultivar per condition, resulting in 33 samples in summary. Each samples is a pool of 5 individual replicates.

first: Dirk

last: Hincha

first: Ellen

last: Zuther


title: Transcriptomic signatures of villous cytotrophoblast and syncytiotrophoblast in term human placenta.

city: PARIS

first: Severine

middle: Aude

last: Degrelle

address: 4 avenue de l'Observatoire

institute: INSERM UMRS-1139

summary: During pregnancy, the placenta ensures multiple functions, which are directly involved in the initiation, fetal growth and outcome of gestation. The placental tissue involved in maternal-fetal exchanges and in synthesis of pregnancy hormones is the mononucleated villous cytotrophoblast (VCT) which aggregates and fuses to form and renew the syncytiotrophoblast (ST). Knowledge of the gene expression pattern specific to this endocrine and exchanges tissue of human placenta is of major importance to understand functions of this heterogeneous and complex tissue. Therefore, we undertook a global analysis of the gene expression profiles of primary cultured-VCT (n=6) and in vitro-differentiated-ST (n=5) in comparison with whole term placental tissue from which mononucleated VCT were isolated. A total of 880 differentially expressed genes (DEG) were observed between VCT/ST compared to whole placenta, and a total of 37 and 137 genes were significantly up and down-regulated, respectively, in VCT compared to ST. The 37 VCT-genes were involved in cellular processes (assembly, organization, and maintenance), whereas the 137 ST-genes were associated with lipid metabolism and cell morphology. In silico, all networks were linked to 3 transcriptional regulators (PPARγ, RARα and NR2F1) which are known to be essential for trophoblast differentiation. Furthermore, a subset of DEG were validated by RT-qPCR or by immunohistochemistry. To conclude, recognition of these pathways is fundamental to increase our understanding of the molecular basis of human trophoblast differentiation. The present study provides for the first time a gene expression signature of the VCT and ST compared to their originated term human placental tissue.

overall_design: One microgram of total RNA from each sample preparation was amplified using the MessageAmp RNA kit  (Ambion), and 3 µg of amplified RNA  (aRNA) was Cy-dye labeled using the CyScribe first-strand cDNA labeling kit  (Amersham Biosciences). To compare the gene expression pattern obtained from each cultured cells (VCT or ST) with the one obtained from corresponding total placental extracts, amplified RNA from cultured cells was labeled with Cy5, while the aRNA from placental tissue was labeled with Cy3. A total of six (VCT) or five (ST) individual cDNA microarrays were performed in this condition.

first: Christine

last: Rouault

first: Karine

last: Clément

first: Mickael

last: Guesnon

first: Corneliu

last: Henegar

first: Marie-Aline

last: Charles

first: Barbara

last: Heude

first: Danièle

last: Evain-Brion

first: Séverine

middle: A

first: Thierry

last: Fournier


title: RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway [Agilent]

status: Public on Jun 30 2016

city: Wuhan, Hubei Province

first: Zhulong

last: Chan

address: Moshan, Wuchang District

department: Wuhan Botanic Garden

institute: Chinese Academy of Sciences

summary: The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. CBFs and CBF regulon genes were down-regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutant plants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 increased the expression of CBFs and CBF regulon genes and decreased cold-induced membrane injury. The rdm4 mutants exhibited decreased antioxidant enzyme activities and increased accumulation of reactive oxygen species. Microarray analysis indicated that a great proportion of genes affected by rdm4 overlapped with those affected by CBF2 and CBF3 in Arabidopsis. Chromatin immunoprecipitation (ChIP) results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF genes but not the promoters of up-stream regulators of CBFs. Together, these data indicate that RDM4 acts as a component of a Pol II transcription complex that regulates CBF gene expression and cold stress resistance in Arabidopsis.

overall_design: Two-week-old seedlings of 35S::RDM4 and Col WT plant were subjected to chilling treatment for 0, 3, and 48 h treatments.Plant materials were then collected for RNA extraction.

first: Jian-Kang

last: Zhu


title: Genomewide copy number profiles for Adenosarcoma patients in Taiwan

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

summary: Müllerian adenosarcomas are malignant gynecologic neoplasms. Advanced disease stage and sarcomatous overgrowth predict aggressive clinical courses. We conducted this study to characterize the genomewide copy number variations (CNV) in adenosarcomas. Paraffin samples from 13 cases were subjected to CNV analysis using OncoScan® FFPE Assay Kit. CNVs were significantly higher in cases with sarcomatous overgrowth. Frequent amplifications of chromosomal segments in 12p12.3 and 12q13.3-23.3 were noted, involving established or potential oncogenes including PIK3C2G (5 cases), MDM2, CPM, YEATS4, CDK4, GLI1, DDIT3 (co-amplified in 4 cases), as well as HMGA2 in 3 cases. MDM2 and CDK4 amplification was verified by fluorescence in situ hybridization.

overall_design: A total of 16 formalin-fixed paraffin-embedded tumor samples from different patients were subjected to genomic DNA extract and SNP array using the novel molecular inversion probe-based OncoScan FFPE Assay Kit (Affymetrix, Santa Clara, California, USA). The raw probe intensity was recorded by using the scanner. Subsequently, intensity value was transformed into copy number by using the official software, Oncoscan Console, provided by Affymetrix Inc. (Santa Clara, CA, USA). The reference model was also provided by the Affymetrix Inc., which included 390 formalin-fixed and paraffin-embedded (FFPE) samples.

first: Jen-Chieh

last: Lee

first: Kuan-Ting

last: Kuo


title: Inflammatory stimulation of zebrafish (Danio rerio) tissues using lipopolisaccharyde.

status: Public on Sep 18 2016

city: Leiden

first: Gabriel

last: Forn-Cuní

state: Zuid-Holland

address: Einsteinweg 55

department: IBL-ASH-CO

institute: Universiteit Leiden

summary: We analyzed if genomic responses of adult zebrafish tissues can reproduce the mammalian known inflammatory process induced by acute endotoxin stress. Although the strength of the inflammatory process was influenced by tissue nature, gene regulation was well conserved across evolution and  zebrafish genomic responses highly correlated with mammals’ inflammatory reactions after lipopolysaccharide stimulation.

overall_design: 10 μg of pure LPS (Sigma) or PBS was intraperitoneally injected to healthy fish and livers, kidneys and muscle were sampled and pooled at 3 hours post injection to analyse the inflammatoy response.

first: Monica

last: Varela

first: Antonio

last: Figueras

first: Beatriz

last: Novoa


title: The methylome and transcriptome of murine foetal skin and scarless wound healing

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

institute: Gdansk University of Technology

overall_design: Refer to individual Series


title: 24h-response to bevacizumab erlortinib in non-small cell lung cancer from blood-based exon array profiling

city: St. Gallen

first: Florent

last: Baty

address: Rorschacherstrasse 95

department: Lung Center

country: Switzerland

institute: Cantonal Hospital St. Gallen

summary:
The mechanisms of action of the combined targeted therapy bevacizumab erlotinib in late stage non-squamous non-small cell lung cancer was investigated by means of whole genome exon arrays.
mRNA from peripherial blood was extracted at baseline and 24h after initiation of the therapy and hybridized on Affymetrix Human Exon 1.0 ST Arrays

overall_design: Prospective phase II trial investigating the efficacy and safety of bevacizumab erlotinib in non-small cell lung cancer

first: Martin

last: Brutsche

first: Francesco

last: Zappa


title: microRNAs differentially regulated in organoids derived from tumors of Apc-deficient mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: microRNA expression profiles were investigated in organoids derived from tumors of Apc-deficient mice and normal intestinal epitehlia of wild-type mice.

overall_design: Intestinal tumor organoids were established from tumors of ApcMin mice. microRNA expression profiles were analyzed by microarray in organoids derived from tumors of ApcMin mice and intestinal epitehlia of wild-type mice.

first: Yoshimasa

last: Saito

first: Toshiaki

last: Nakaoka


title: Gene expression changes in response to the overexpression of the Arabidopsis SMB gene, and simultaneous loss of SMB, BRN1 and BRN2 functions

status: Public on Oct 31 2016

city: Ikoma

first: Keiji

last: Nakajima

state: Nara

address: 8916-5 Takayama

department: Graduate School of Biological Sciences

institute: Nara Institute of Science and Technology

summary: The Arabidopsis NAC transcription factors SOMBRERO (SMB), BEARSKIN1 (BRN1) and BEARSKIN2 (BRN2) regulate root cap differentiation. In order to identify genes acting downstream of these transcription factors comparable transcriptome analyses were carried out using Agilent expression arrays.

overall_design: Transcriptomes were compared between SMB-overexpressing roots and controls root, as well as between wild-type roots and smb brn1 brn2 triple mutant root. For each comparison dye-swapped replicates were performed using independently isolated RNA pools.


title: Transcriptome analysis of response to infection of cassava anthracnose disease (CAD) using an oligo-DNA microarray from cassava

status: Public on Dec 31 2016

city: Yokohama

first: Tetsuya

last: Sakurai

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

summary: Cassava Anthracnose Disease (CAD) that caused by the fungus Colletotorichum anthracnose is a serious disease of cassava in worldwide. In this study, we aim to establish the cassava oligo-DNA microarray representing approximately 30,000 cassava genes and apply it to investigate the molecular mechanisms against fungal infection using two cassava cultivars; Huay Bong 60 (HB60, resistant line for CAD) and Hanatee (HN, sensitive line for CAD). Based on expression profiling, we showed that the expression of various biotic stress-inducible genes, such as detoxification enzyme related genes is higher in HB60 under the treated conditions and non-treated condition, compared with HN. These results show that stress-inducible signaling pathways including ROS detoxification are constitutively activated in HB60 even under normal growth conditions without stress. These results suggest that our microarray is a useful tool for analyzing the cassava transcriptome and add new insight into the host responses of cassava against fungal infection.

overall_design: After cutting, the cassava plants were grown under natural light and temperature conditions in a greenhouse of Mahidol University in Thailand for about 8 weeks. The cassava plants were inoculated at the inter-nodal regions by stem puncture. Then total RNA was prepared from the leaves and used for the microarray hybridization. Three replicative hybridization experiments were carried out using the independent biological samples.

first: Yoshinori

last: Utsumi

first: Maho

last: Tanaka

first: Atsushi

last: Kurotani

first: Takuhiro

last: Yoshida

first: Keiichi

last: Mochida

first: Akihiro

last: Matsui

first: Manabu

last: Ishitani

first: Supajit

last: Sraphet

first: Sukhuman

last: Whankaew

first: Jarunya

last: Narangajavana

first: Kanokporn

last: Triwitayakorn

first: Motoaki

last: Seki


title: Expression changes by Endodermal PIF1: SCR:PIF1/pifQ transgenic plant vs. pif1pif3pif4pif5 (pifQ) mutant

status: Public on Aug 01 2016

city: Daejeon

first: Keunhwa

last: Kim

address: 291 Daehak-ro

department: Biological Sciences

institute: KAIST

summary: Transcriptional profiling of dark-grown Arabidopsis seedlings comparing SCR:PIF1/pifQ transgenic plant with pif1pif3pif4pif5 quadruple mutant (pifQ). Seedlings were grown under dark condition for 2.5 days. Goal was to determine the effects of endodermal PIF1 in dark-grown seedlings.

overall_design: Two-condition experiment, SCR:PIF1/pifQ vs. pifQ Biological replicates: 3 pifQ replicates, 3 SCR:PIF1 replicates.

first: Giltsu

last: Choi


title: Salt stress responses of Arabidopsis thaliana and Eutrema salsugineum (Thellungiella salsuginea)

status: Public on Jun 29 2016

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

summary: Arabidopsis thaliana is a glycophyte with a low salt tolerance, while Eutrema is a halophyte with a very high salt tolerance. To elucidate the transcriptional basis of this difference, we performed hydroponis culture experiments where we grew plants under control conditions (25 mM NaCl) or under salt stress (200 mM NaCl for both species, 500 mM for Eutrema). Salt concentration was increased for the stress treatments by increments of 50 mM per day (25 mM on the first day). Plants were grown at the final NaCl concentration for an additional week, when rosettes were harvested for RNA isolation.Expression patterns were compared between treatments and between species.

sample_organism:
Arabidopsis thaliana
Eutrema salsugineum

overall_design: In total, 15 samples were hybridized. They were derived from three independent biological experiments (replicate_1 to replicate_3). Controlds were grown at 25 mM NaCl, salt stressed plants at either 200 mM NaCl or 500 mM NaCl.

first: Yang

last: Lee

first: Dirk

last: Hincha


title: Using Mass Cytometry and In vivo Imaging to Study Emergency Repopulation of Immune Cells in Murine Liver

status: Public on Jun 12 2016

city: Boston

first: Laura

last: Cox

state: MA

address: 77 Avenue Louis Pasteur

department: Neurology

institute: Brigham and Women's Hospital

summary: Macrophages and dendritic cells are phagocytes present in almost all tissues in mammals and play a pivotal role for tissue homeostasis and during immune responses. Liver phagocytes play a pivotal role in host immune responses and exquisite mechanisms are necessary to govern the density and the location of the different hepatic leukocytes. However in catastrophic events including trauma, infections or toxin ingestion, many of the liver phagocytes can be wiped out leaving large areas devoid of these cells. Here we used a unique combination of mass cytometry (CyTOF), gene expression and liver intravital approaches to precisely determine phagocytic populations within the liver and the functional consequences of their replenishment by myeloid precursors. While Kupffer cells were exclusively located in the sinusoidal lumen, we identified a population of dendritic cells that was mainly located under the liver capsule. After full depletion of dendritic and Kupffer cells, intravascular myeloid precursors replenished location, density and function of both populations. However, these emergency repopulated livers were dysfunctional in their ability to respond to injury and to clear bacteria for at least 30 days. After this “educational period”, new phagocytes returned to normal response to injury and bacterial trapping. Conclusions: Our data shed light on the liver’s ability to locally shape phagocyte precursors into two vastly different immune cells localized to two fundamentally different tissue compartments.

overall_design: 4 different cell types were isolated from mice, RNA was extracted, and gene expression was measured using the Nanostring nCounter Mouse Immunology Panel

first: Bruna

last: David

first: Rafael

last: Rezende

first: Maisa

last: Atunes

first: Monica

last: Santos

first: Ariane

last: Diniz

first: Rafaela

last: Pereira

first: Sarah

last: Marchesi

first: Debora

last: Alvarenga

first: Brenda

last: Nakagaki

first: Alan

last: Araujo

first: Daniela

last: Reis

first: Renata

last: Rocha

first: Pedro

last: Marques

first: Woo-Yong

first: Justin

last: Deniset

first: Pei

last: Liew

first: Stephen

last: Rubino

first: Vanessa

last: Pinho

first: Thiago

last: Cunha

first: Gabriel

last: Fernandes

first: Andre

last: Oliveira

first: Mauro

last: Teixiera

first: Paul

last: Kubes

first: Gustavo

last: Menezes


title: TNFalpha and IL-6 induced anorexia: effects on serotonin turnover

status: Public on May 31 2016

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

institute: Wageningen University

summary: Anorexia can occur as a serious complication of chronic disease. Increasing evidence suggests that inflammation plays a major role, along with a hypothalamic dysregulation characterized by locally elevated serotonin levels. The present study was undertaken to further explore the connections between peripheral inflammation, anorexia and hypothalamic serotonin metabolism and signaling pathways. We studied transcriptomic changes and serotonergic activity in the hypothalamus of mice after an intraperitoneal injection with TNFα, IL-6 or a combination of TNFα and IL-6.

overall_design: C57BL/6 mice were intraperitoneally injected with TNFalpha, IL-6 Low, IL-6 High, combination TNF+IL-6 Low or combination TNF+IL-6 High. Each group comprised of 12 animals, of which 6 animals were used for transcriptomics.

first: Jvalini

last: Dwarkasing

first: Renger

last: Witkamp

first: Mark

last: Boekschoten

first: Marjolein

last: ter Laak

first: Gunnar

last: Flik

first: Klaske

last: van Norren


title: Expression data of the BMDMs from GPS2 WT and MKO mice

status: Public on Jun 06 2016

city: Huddinge

first: Eckardt

last: Treuter

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

institute: Karolinska Institute

summary:
Obesity is a major risk factor for metabolic disorders like insulin resistance and diabetes. We previously identified GPS2 as a clinical relavant repressor of metaflammation. No animal KO models were used to study its physiological function in vivo. The role of GPS2 in macrophage activation and inflammation is also largely unknown.
Here we developed a GPS2 myeloid specific KO mice to study the regulation of GPS2 in macrophage inflammation.  We found GPS2 ablation was linked with significant upregulation in inflammation markers in BMDMs from this array.

overall_design: WT and GPS2 KO BMDMs were differentiated and cultured. Total mRNA was extracted from unstimulated BMDM (n=3 in each group) and hybridized on affymetrix microarrays.

first: Rongrong

last: Fan

first: Anastasios

last: Damdimopoulos