title: Transcriptional regulatory networks controlling woolliness in peach in response to gibberellin application and cold storage

status: Public on Oct 29 2015

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary: Cold storage (CS) is widely used to extend fruit postharvest. In peach, chilling injuries may cause intense juice loss leading to a dry ‘woolly’ texture of the fruit flesh. The disturbance, named woolliness, is associated to abnormal pectin metabolism and results in anatomical and physiological alterations. Application of gibberellic acid (GA) at the initial stages of pit hardening has been shown to impair woolliness incidence, however the mechanisms controlling the response remain unknown. We have employed genome wide transcription analyses to investigate the effects of GA application and CS of peaches. Approximately half (48.26%, 13846) of the investigated genes exhibited significant differential expression in response to the treatments. Gene ontology classes associated to cellular and developmental processes were overrepresented among the differentially regulated genes, whereas sequences classified in cell death and immune response categories were underrepresented. Gene set enrichment analyses demonstrated a predominant role of CS in repressing the transcription of genes associated to cell wall metabolism. In contrast, genes involved in hormone metabolism and signaling exhibited a more complex transcriptional response to the factors, indicating an extensive network of crosstalk between GA and low temperatures. Time course transcriptional profiling analyses also confirmed the involvement of cell wall metabolism genes in woolliness onset in peach. Overall, our results provide further insights on the mechanisms controlling the complex phenotypes associated to postharvest textural changes in peach.

overall_design: Four samples (CONT, CONTcs, GA3, GA3cs), each with three biological replicates (R1, R2 and R3), were analyzed. Control samples (CONT and CONTcs) consist of peach mesocarp not treated with GA3 at pit hardening, and either assayed at harvest (CONT) or after 15 days of cold storage (CONTcs). GA3 samples (GA3 and GA3cs) consist of peach mesocarp treated with GA3 at pit hardening, and either assayed at harvest (GA3) or after 15 days of cold storage (GA3cs).

first: Camila

last: Pegoraro

first: Alice

last: Tadiello

first: Cesar

middle: L

last: Girardi

first: Fabio

last: Chaves

first: Vera

last: Quecini

first: Antonio

last: Costa de Oliveira

first: Livio

last: Trainotti

middle: V

last: Rombaldi


title: Effect of litter birth weight phenotype on transcriptomic response to swine influenza virus infection in pig lung

status: Public on Oct 27 2015

city: Edmonton

first: James

middle: Michael

last: Wilkinson

state: Alberta

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

country: Canada

institute: University of Alberta

summary: Analysis of gene expression in the lungs of pigs from high and low litter birth weight groups (HBW and LBW) inoculated with swine influenza virus. The aim of the experiment is to determine whether litter birth weight has an effect on the innate immune response to infection in pigs, and whether differences in gene expression can be linked to epigenetic differences between the two birth weight groups.

overall_design: A two condition experiment: lung tissue RNA from HBW and LBW SIV-infected pigs. 16 biological replicates for each condition, each hybridized with a reference to separate arrays. 32 arrays in total.

first: Jamie

first: George

last: Foxcroft

first: Graham

last: Plastow

first: John

last: Harding

first: Rayna

last: Gunvaldsen

first: Susan

last: Detmer

first: Walter

last: Dixon

first: Michael

last: Dyck


title: Enhanced sucrose loading improves rice yield by increasing grain size

status: Public on Oct 21 2015

city: Beijing

first: Congming

last: Lu

state: Beijing

address: Haidian Xiangshan Nanxincun 20#

department: The Key Laboratory of Photobiology, CAS

country: China

institute: Institute of Botany, CAS

summary: Transgenic rice plants expressing the Arabidopsis phloem-specific sucrose transporter AtSUC2, which loads Suc into the phloem, showed an increase in grain yield of up to 16% relative to wild-type plants in field trials. The goal was to reveal how expressed AtSUC2 in rice leads to increased grain yield analyzing global gene expression.

overall_design: Microarray analyses were performed on flag leaves and developing seeds between wild-type plants (WT) and transgenic plants (line 51) on the 10th day after fertilization, i.e. flag leaves of WT versus flag leaves of line 51; developing seeds of WT versus developing seeds of line 51. Three biological replicates were performed for flag leaves and developing seeds between WT and line 51.

first: Liang

last: Wang

first: Qingtao

first: Xiaogang

last: Wen

first: Conming


title: The effect of 12-HHT/BLT2 receptor axis on the global  gene expression after calcium switch in MDCK cells

status: Public on Oct 20 2015

city: Tokyo

first: Takehiko

last: Yokomizo

address: Hongo 2-1-1, Bunkyo-ku

department: Biochemistry

country: Japan

institute: Juntendo University School of Medicine

summary: Examination of global gene expression in BLT2 overexpressing MDCK (MDCK-BLT2) cells and Mock-MDCK cells before and after calcium switch.

overall_design: After MDCK cells reached confluence, culture medium (DMEM (WAKO) containing 10% FCS) was replaced to calcium-free medium SMEM (Gibco) and incubated for 2 h or 18 h. After incubation for 18 h, SMEM was changed to high-calcium medium DMEM (WAKO) with or without 200 nM 12-HHT, and the cells were incubated for 2 h. Total RNA was prepared from MDCK cells using TRIzol Reagent (Life Technology).  Total RNA from triplicate samples was mixed to reduce the difference among the samples, and subsequently used for labeling. cDNA was generated and labeled with The Ambion WT Expression Kit and GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturer's protocols. The labeled samples were subjected to hybridization with GeneChip Canine Gene 1.0 ST Array (Affymetrix) and GeneChip Hybridization, Wash, and Stain Kit (Affymetrix). The signals were scanned using the GeneChip Scanner 3000 7G, and the data were analyzed using Affymetrix Expression Console Software.

first: Yumiko

last: Abe

first: Kazuko

last: Saeki


title: Epithelial-mesenchymal transition in the differentiation of cyto- to extravillous trophoblast

status: Public on Oct 15 2015

city: Maplewood

first: Nick

last: Illsley

state: NJ

address: Richmond Ave

country: USA

institute: Placental Research Group LLC

summary: The transformation of cytotrophoblast (CTB) to extravillous trophoblast (EVT) is an essential process for placental implantation. EVT generated at the tips of the anchoring villi migrate away from the placenta and invade the endometrium and maternal spiral arteries, where they modulate maternal immune responses and remodel the arteries into high-volume conduits to facilitate uteroplacental blood flow. The process of EVT differentiation has several factors in common with the epithelial-to-mesenchymal transition (EMT) observed in embryonic development, wound healing and cancer metastasis. We hypothesized that the generation of invasive EVT from CTB was a form of EMT. We isolated paired CTB and EVT from first trimester placentae by flow cytometry for integrin beta 4 (CTB) and HLA-G (EVT). We compared their gene expression using a PCR array comprising probes for genes involved in EMT. Out of 84 genes, 24 were down-regulated in EVT compared to CTB, including epithelial markers such as E-cadherin (-11-fold) and occludin (-75-fold). Another 30 genes were up-regulated in EVT compared to CTB including mesenchymal markers such as vimentin (235-fold) and fibronectin (107-fold) as well as the matrix metalloproteinases, MMP2 and MMP9 (357-fold, 129-fold). These alterations also included major increases in the ZEB2 (zinc finger E-box binding homeobox 2, 198-fold) and TCF4 (transcription factor 4, 18-fold) transcription factors, recognized as EMT master regulators, suggesting possible stimulatory mechanisms. There was substantial up-regulation of the genes encoding TGFb1 and TGFb2 (48-fold, 115-fold), which may contribute to the maintenance of the mesenchymal-like phenotype. We conclude that transformation of CTB to EVT is consistent with an EMT, although the differences with other types of EMT suggest this may be a unique form

overall_design: Paired sets of CTB and EVT obtained from single placenta by fluorescence activated cell sorting (integrin beta4, CTB; HLA-G, EVT). RNA extracted from paired sets obtained from 6 separate placentae ranging from 6-10 weeks gestational age and reverse-transcribed, pre-amplified and analyzed on a PCR Array containing probes for 84 genes associated with the EMT (SABiociences, RT2 Profiler PCR Array Cat# PAHS-090Z).  Relative gene expression determined for EVT compared to CTB.

first: Nicholas

middle: P

first: Joanna

last: James


title: miRNA profiling for mouse B10+ cells and B10- B cells

city: New York

first: Jianbo

last: Sun

state: NY

department: Microbiology and Immunology

institute: Columbia University

summary: we used genome-wide transcriptome analysis to profile the mRNA, long noncoding RNA (lncRNA), and microRNA (miRNA) expression of B10 cells, an antigen-specific Cd1dhiCd5+Cd19hiIl10 competent regulatory B cell. Potential key upstream regulators (including transcription factors, cytokines, trans-membrane receptors, and kinases) for Breg biogenesis and function were identified.

overall_design: B10+ B cells (Cd1dhiCd5+Cd19hiIl10+) and B10- cells (Cd1d-Cd5-Cd19hiIl10-) from mouse splenic B cell were sorted for RNA preparation. Two independent repeats were prepared for microarray analysis

first: Uttiya

last: Basu


title: Transcriptional profile Lactobacillus plantarum WCFS1 : 1.5mM gallic acid (GA) treated cells

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

country: Spain

institute: ICTAN-CSIC

summary: Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with 1.5 mM gallic acid (GA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in transport and decarboxilation of gallic acid.

overall_design: Biological triplicates: untreated cells: Control vs. 1.5 mM gallic acid treated cells: Experimental

first: Inés

last: Reverón

first: Blanca

last: de las Rivas

first: Rosario

last: Muñoz

first: Félix

last: López de Felipe


title: The CaSm (LSm1) oncogene promotes transformation, chemoresistance, and metastasis of pancreatic cancer cells

status: Public on Oct 24 2015

city: Charleston

first: Elizabeth

last: Little

state: SC

address: 86 Jonathan Lucas St

department: Surgery

institute: Medical University of South Carolina

summary:
The Cancer associated Sm-like (CaSm) oncogene is overexpressed in 87% of human pancreatic tumor samples and CaSm knockdown has demonstrated therapeutic efficacy in murine models of pancreatic cancer. Evidence indicates that CaSm modulates mRNA degradation; however, its target genes and the mechanisms by which CaSm promotes pancreatic cancer remain largely unknown.  Here, we demonstrate that the CaSm overexpression alters several hallmarks of cancer – including transformation, proliferation, chemoresistance, and metastasis.
Doxycycline-induced CaSm expression enhanced proliferation and both anchorage-dependent and -independent growth of the human Panc-1 cells in vitro.  CaSm induction decreased gemcitabine-induced cytotoxicity and altered the expression of apoptotic regulation genes, including Bad, E2F1, and Bcl-XL. CaSm-overexpressing Panc-1 cells were 2-fold more migratory and 4-fold more invasive than the driver controls and demonstrated characteristics of epithelial-to-mesenchymal transition such as morphological changes and decreased E-cadherin expression. CaSm induction resulted in changes in RNA expression of metastasis-associated genes such as MMP1, SerpinB5, uPAR, and Slug. Using a murine model of metastatic pancreatic cancer, injection of CaSm-induced Panc-1 cells resulted in a higher abundance of hepatic metastatic lesions.    Overall, CaSm overexpression contributed to a more aggressive cancer phenotype in Panc-1 cells, further supporting the use of CaSm as a therapeutic target against pancreatic cancer.

overall_design: Tet-on driver and tet-on CaSm Panc-1 cells were grown with and without doxycycline (1 μg/mL) for 4 weeks.  Levels of CaSm expression were confirmed using RT-PCR (Supplementary Figure 2a).  RNA isolation was performed using RNeasy Plus kit (Qiagen, Valencia, CA) following the manufacturer’s protocols. The Hollings Cancer Center Tissue Biorepository core facility confirmed RNA quality using the 18S/28S Ratio Integrity Number using Agilent 2100 Bioanalyzer  (Agilent Technologies, Santa Clara, CA); RNA with a RIN of 10 was used for further analysis (Supplementary Figure 2b).  Complement DNA synthesis was performed using RT2 First Strand kit and RT2  SYBR Green qPCR master mix was used for the microarray master mix reagent according to the manufacturer’s manual (SABiosciences).  The Cancer PathwayFinder PCR array (SABiosciences) was run on the Roche 480 Lightcycler (Roche, Indianapolis, IN) with 2 plates run for each tet-on driver + doxycycline, tet-on CaSm, and tet-on CaSm + doxycycline.  The plates included controls for genomic DNA contamination, reverse transcription, and positive controls.  Analysis was performed using SABioscience’s Free PCR Array Data Analysis Software (ΔΔCt method) with B2M, HPRT1, and GAPDH as pooled housekeeping genes.

middle: C

first: David

middle: J

last: Cole


title: A set of differentially expressed cerebro-spinal fluid (CSF) miRNAs can diagnose CNS malignancies

city: Columbus

first: Alessandra

last: Drusco

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

summary: We analyzed 80 patients’ CFS by Nanostring, and validated a microRNA profile that can differentiate between and among some classes of CNS tumors.

overall_design: A total of 80 CSF samples were collected from the Regina Elena Institute, Rome, Italy  and from The Ohio State University, Columbus, OH. Sixty-six samples came from patients with benign and malignant brain lesions, while 14 from patients without brain disease.

first: A

first: C

middle: M

last: Croce


title: Transcriptomic analysis of pigs exhibiting differential susceptibility to swine influenza (SIV) pathology in the lung

first: James

last: Wilkinson

type:
Expression profiling by array
Third-party reanalysis

summary: Comparison of gene expression in the lungs of pigs classified as Resistant (RES) or Susceptible (SUS) to influenza pathology based on clinical lesion scores. The aim of the experiment is to identify genes whose expression is associated with resistance/susceptibility to influenza pathology. These are a subset of animals selected from a larger experiment that investigated the effect of low (LBW) or high (HBW) litter birth weight phenotype on influenza pathology.

overall_design: A two condition experiment: lung tissue RNA from RES and SUS SIV-infected pigs. 6 biological replicates for each condition, each hybridized with a reference to separate arrays. 12 arrays in total.

first: Jamie

first: George

last: Foxcroft

first: Graham

last: Plastow

first: John

last: Harding

first: Rayna

last: Gunvaldsen

first: Susan

last: Detmer

first: Walter

last: Dixon

first: Michael

last: Dyck


title: Expression data from leaves of Hordeum vulgare at seedling stage

status: Public on Oct 08 2015

city: Hangzhou

first: Hongyan

last: Sun

address: Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University

institute: Zhejiang University

summary:
A DNA microarray analysis detected large-scale changes of gene expression in response to Cd stress with a substantial difference between the two barley genotypes differing in Cd tolerance and accumulation. Cd stress led to higher expression of genes involved in transport, carbohydrate metabolism and signal transduction in the low-grain-Cd-accumulating genotype. Novel transporter genes such as zinc transporter genes were identified as being associated with low Cd accumulation.
We used microarrays to understand the mechanism of low Cd accumulation in crops which is crucial for sustainable safe food production in Cd-contaminated soils.

overall_design: Barley leaves were selected at seedling stage in hydroponic experiment for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain genes that were distinct differences in gene expression between the two genotypes after Cd treatment. To that end, we hand-selected barley leaves under control and Cd treatment conditions of two genotypes, i.e. leaves under control in low-grain-Cd-accumulating and Cd-sensitive genotyp W6nk2, leaves under control in high-grain-Cd-accumulating and tolerant genotype Zhenong8, Cd treated leaves in W6nk2, and Cd treated leaves in Zhenong8.

first: Feibo

last: Wu


title: Transcriptomic analysis of trout gill ionocytes in freshwater and seawater using laser capture microdissection combined with microarray analysis

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

summary: Fish gills represent a complex organ that perform multiple physiological functions and is composed of several cell types. Among these cells, ionocytes are implicated in the maintenance of ion homeostasis. However, because the ionocyte represents only a small percent of whole gill tissue, its specific transcriptome can be overlooked among the numerous cell types included in the gill. The objective of this study is to better understand ionocyte functions by comparing the RNA expression of this cell type in freshwater and seawater adapted rainbow trout. To realize this objective, ionocytes were captured from gill cryosections using laser capture microdissection after immunohistochemistry. Then, transcriptome analyses were performed on an Agilent trout oligonucleotide microarray. Gene expression analysis identified 108 unique annotated genes differentially expressed between freshwater and seawater ionocytes, with a gene fold higher than 3. Most of these genes were up regulated in freshwater cells. Interestingly, several genes implicated in ion transport, extracellular matrix and structural cellular proteins appeared up regulated in freshwater ionocytes. Among them, several ion transporters, such as CIC2, SLC26A6, and NBC, were validated by qPCR and/or in situ hybridization. The latter technique allowed us to localize the transcripts of these ion transporters in only ionocytes and more particularly in the freshwater cells. Genes involved in metabolism and also several genes implicated in transcriptional regulation, cell signaling and the cell cycle were also over-expressed in freshwater ionocytes. In conclusion, laser capture microdissection combined with microarray analysis allowed for the determination of the cell signature of scarce cells in fish gills, such as ionocytes, and aided characterization of the transcriptome of these cells in freshwater and seawater adapted trout.

overall_design: Gene expression of gill ionocytes, isolated by immuno-laser capture microdissection, was measured from 4 freshwater and 4 seawater adapted rainbow trout.

first: Isabelle

last: Leguen

last: Le Cam

first: Jerome

last: Montfort

first: Sandrine

last: Peron

first: Alain

last: Fautrel


title: Mucosal vaccination with attenuated Mycobacterium tuberculosis induces strong central memory responses and protects against tuberculosis

status: Public on Oct 02 2015

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

summary: This submission includes DNA microarray gene expression data from two sets of experiments where bronchoalveolar lavage cell transcription from rhesus macaques vaccinated via aerosols with either BCG or attenuated MtbDsigH mutant were compared to unvaccinated (naive samples) using two color arrays

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Two color Agilent 4x44k arrays were run to compare the gene-expression in BAL samples derived from three BCG (aerosol) vaccinated and three MtbDsigH (aerosol) vaccinated Indian rhesus macaques. The baseline in the experiment was BAL from the same animals prior to infection and the experimental post-vaccination BAL was derived at week 3.

first: Smriti

last: Mehra


title: Transcriptomic analysis of Oenococcus oenos response to ethanol shock

status: Public on Oct 01 2015

city: Tarragona

first: Cristina

last: Reguant

state: Tarragona

address: Marcel·lí Domingo 1

department: Biochemistry and Biotechnology

institute: University Rovira i Virgili

summary: The correct development of malolactic fermentation depends on the capacity of Oenococcus oeni to survive under harsh wine conditions. The presence of ethanol is one of the most stressful factors affecting O. oeni performance. In this study, the effect of ethanol addition (12% vol/vol) on O. oeni PSU-1 has been evaluated using a transcriptomic approach.

overall_design: Oenococcus oeni PSU-1 was grown in rich medium and after treated with the addition of ethanol (12% v/v) or the same volume of water. Samples were taken 1 and 3 hours after the treatment. Total RNA was analysed using a custom designed expression microarray.

first: Albert

last: Bordons

first: Nair

last: Olguín

first: Ricardo

last: Cordero


title: Substantial Reprogramming of the Thellungiella salsuginea Transcriptome in Response to UV and Silver Nitrate Challenge

city: Freising

first: Erich

last: Glawischnig

address: Emil-Ramann-Str. 8

department: Plant Science

country: Germany

institute: TU Muenchen

summary: The transcriptional response of T. salsuginea to UV irradiation and AgNO3 was monitored by microarray analysis. Most transcripts (respectively 70% and 78%) were significantly differentially regulated and a large overlap between the two treatments was observed (54% of total). While core genes of the biosynthesis of aliphatic glucosinolates were repressed, tryptophan and indole glucosinolate biosynthetic genes, as well as defence-related WRKY transcription factors, were consistently upregulated.

overall_design: Microarray analysis of four biological replicates was conducted with Agilent arrays. Statistically robust differential regulation was observed for the majority of transcripts.

first: Stefanie

last: Mucha

first: Dirk

last: Walther

first: Teresa

last: Müller

first: Dirk.

middle: K

last: Hincha


title: The transcriptome of muscle and liver is responding differently to a combined trenbolone acetate and estradiol implant in cattle

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

summary: In the present study, an attempt to compare bovine transcriptome of two different tissue matrices (liver and muscle) treated with the same molecules (trenbolone acetate (TBA) and estradiol (E2)) was carried out in order to understand the response of different tissues to the same treatment on a genomic/transcriptomic level. The primary aim of this study was to compare, via transcriptomic approach, the response of both muscle and liver to anabolic steroids, and to point out the main differences and similarities between both matrices. In addition, a second aim was to list out the main differentially expressed (DE) genes that can be used as a “pool” for biomarker investigations in the future. A bovine oligo microarray platform (GPL7053) was used to profile gene expression from thirty (30) bovine liver and muscle (biceps brachii) samples. Isolated and purified total RNAs were individually hybridized to the Agilent bovine V1 4x44k DNA microarray. The comparison of untreated and treated bovine transcriptomes revealed a set of differentially expressed genes. After functional analysis and qPCR validation, the result showed that the two transcriptomes showed completely different patterns, in terms of altered pathways and involved biological processes, following the treatment with anabolic steroids. However, they had 20 commonly expressed genes in-between.

overall_design: A total of 30 animals was used in this study. Animals were randomly divided into two groups of 15 animals each. The first group was used as a control (CTRL), the second was treated for 71 days with 200 mg trenbolone acetate (TBA) + 40 mg estradiol (E2) formulated together in a slow-release subcutaneous ear implant. Following completion of the treatment, animals were slaughtered and tissue aliquots from both liver and muscle tissues were taken and stored for further use. All samples yielded high quality RNA that was tested prior the microarray setup.

first: Mery

last: Giantin

first: Mauro

last: Dacasto


title: Shugoshin forms a specialized chromatin domain at subtelomeres that regulates transcription and replication timing.

city: Kami

first: Kojiro

last: Ishii

state: Kochi

address: 185 Miyanokuchi, Tosayamada

institute: Kochi University of Technology

type: Genome binding/occupancy profiling by genome tiling array

summary: A chromosome is composed of structurally and functionally distinct domains. However, the molecular mechanisms underlying the formation of chromatin structure and the function of subtelomeres, the telomere-adjacent regions, remain obscure. Here we report the roles of the conserved centromeric protein Shugoshin 2 (Sgo2) in defining chromatin structure and functions of the subtelomeres in the fission yeast Schizosaccharomyces pombe. We show that Sgo2 localizes at the subtelomeres preferentially during G2 phase and is essential for the formation of a highly condensed subtelomeric chromatin body 'knob'. Furthermore, the absence of Sgo2 leads to the derepression of the subtelomeric genes and premature DNA replication at the subtelomeric late origins. Thus, the subtelomeric specialized chromatin domain organized by Sgo2 represses both transcription and replication to ensure proper gene expression and replication timing.

overall_design: Chromosomal distribution of Sgo2 protein in S. pombe

first: Junko

last: Kanoh


title: Responses of Streptococcus gordonii to arginine restriction

city: Newcastle

first: Matthew

last: Bashton

address: Newcastle

country: United Kingdom

institute: Newcastle Univerity

summary: Our previous work has indicated that extracellular arginine concentrations may be an important stimulus for gene regulation in S gordonii.  Here cells were cultured in a chemically defined medium (CDM) to mid exponential phase .  Cultures were split and resuspended in either CDM or CDM lacking arginine.  After 30 mins RNA was extracted and gene expression was monitored using an Agilent microarray.

overall_design: Single colour microarrays were used to measure gene expression in four biological replicates of S gordonii cells cultured, with and without arginine restriction.

first: Nick

last: Jakubovics


title: Transcriptional profile Lactobacillus plantarum WCFS1: 15 mM gallic acid (GA) treated cells

first: Felix

last: Lopez de Felipe

summary: Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with gallic acid (GA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in transport and decarboxilation of gallic acid.

overall_design: Biological triplicates: untreated cells: Control vs. gallic acid treated cells: Experimental

first: Inés

last: Reverón

first: Blanca

last: de las Rivas

first: Rosario

last: Muñoz

first: Félix

last: López de Felipe


title: Preimplantation stage-specific effect of culture environment on the DNA methylome of bovine blastocysts

status: Public on Oct 07 2015

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

institute: University of Bonn

type: Methylation profiling by genome tiling array

summary: The culture conditions of the early preimplantation embryos affects the DNA methylation landscape of the resulting blastocysts.

overall_design: Five groups of blastocysts were generated. The first (ZY), second (4C) and third (16C) blastocysts groups were obtained after transfer of in vitro developed zygote, 4-cell and 16-cell stage embryos, respectively to synchronized Simmental heifers followed by blastocysts recovery at day 7 of the estrous cycle. The fourth (IVP) and the fifth (VO) blastocyst groups represent those produced completely under in vitro and in vivo culture conditions, respectively. The global DNA methylation pattern of  ZY, 4C, 16C and IVP blastocyst groups  was investigated with reference to the VO group using EDMA array.

first: Eric

last: Fournier

first: Michael

last: Hoelker

first: Mohammed

last: Saeed-Zidane

first: Ernst

last: Tholen

first: Christian

last: Looft

first: Christiane

last: Neuhoff

first: Urban

last: Besenfelder

first: Vita

last: Havlicek

first: Franca

last: Rings

first: Dominic

last: Gagné

first: Marc-André

last: Sirard

first: Claude

last: Robert

first: Ahmed

last: Gad

first: Karl

last: Schellander

first: Dawit

last: Tesfaye


title: Longitudinal Studies of a B-Cell-Derived Signature of Tolerance in Renal Transplantation

status: Public on Sep 30 2015

city: Bethesda

first: Adam

last: Asare

state: MD

address: 7500 Old Georgetown Road, Suite 800

department: Bioinformatics Group

institute: Immune Tolerance Network

summary:
The development of reliable biomarkers of transplant tolerance would enhance the safety and feasibility of clinical trials and potentially also facilitate management of patients on standard immunosuppressive therapies. To this end, we examined peripheral blood samples of spontaneously tolerant renal transplant recipients, as well as patients enrolled in two interventional tolerance trials, using multiparameter flow cytometry and gene expression analysis. Repeat analysis of samples from a previously reported tolerant cohort, as well as newly identified tolerant patients, confirmed that tolerance was associated with increased expression of B cell-associated genes relative to immunosuppressed patients with stable renal function. This was not accounted for merely by an increase in total B cell numbers, but appeared to be the result of increased frequencies of transitional and naïve B cells. Moreover, serial measurements demonstrated that this pattern persisted over several years. Importantly, patients rendered tolerant via induction of transient mixed chimerism, and those weaned to low levels of immunosuppression, showed similar increases in the expression of selected B cell genes as did spontaneously tolerant individuals. Collectively, these findings support the notion that alterations in B cells may be a common theme for tolerant kidney transplant recipients, and a useful immune monitoring tool in prospective trials.
The MassARRAY QGE (Sequenom) multiplexed primer and competitive template designs and analysis were reported previously.

overall_design: Total of 25 TOL (Tolerant), 7 New TOL (New Tolerant), 34 SI (Standard Immunosuppression) in cohort ITN507; 7 Sirolimus Monotherapy, 2 SI Multiagent in cohort ITN013; and 7 TOL and 1 Return to SI in cohorts ITN010 and ITN036.

first: Kenneth

middle: A

last: Newell

first: Ignacio

last: Sanz

first: Chungwen

last: Wei

first: Alexander

last: Rosenberg

first: Zhong

last: Gao

first: Sai

last: Kanaparthi

first: Smita

first: Noha

last: Lim

last: Stahly

last: Howell

first: Stuart

last: Knechtle

first: Allan

last: Kirk

first: William

middle: H

last: Marks

first: Tatsuo

last: Kawai

first: Thomas

last: Spitzer

first: Nina

last: Tolkoff-Rubin

first: Megan

last: Sykes

first: David

last: Sachs

first: A

middle: B

last: Cosimi

last: Burlingham

first: Deborah

last: Phippard

first: Laurence

last: Turka


title: Integrative “omic” analysis reveals distinctive cold responses in leaves and roots of strawberry, Fragaria × ananassa ‘Korona’

status: Public on Sep 29 2015

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: To assess underlying metabolic processes and regulatory mechanisms during cold exposure of strawberry, integrative “omic” approaches were applied to F. ananassa ‘Korona’. Analysis of leaf tissue was emphasized because of its immediate and early responses in the cold acclimation processes. Levels of metabolites, proteins, and transcripts in tissues from plants grown at 20°C were compared to those following 1 to 10 days of cold exposure. When leaves and roots were subjected to GC/TOF-MS-based metabolite profiling, about 160 compounds comprising mostly structurally annotated primary metabolites and secondary metabolites, were found. Overall, ‘Korona’ showed a modest increase of protective metabolites such as amino acids (aspartic acid, leucine, isoleucine, and valine), pentoses, phosphorylated and non-phosphorylated hexoses, and distinct compounds of the raffinose pathway (galactinol and raffinose). Distinctive responses were observed in roots and leaves. By 2DE proteomics a total of 845 spots were observed in leaves; 4.6% changed significantly in response to cold. Twenty-one proteins were identified, many of which were associated with general metabolism or photosynthesis. Transcript levels in leaves were determined by microarray, where dozens of cold associated transcripts were quantitatively characterized, and levels of several potential key contributors (e.g., the dehydrin COR47 and GADb) to cold tolerance were confirmed by qRT-PCR. Cold responses are placed within the existing knowledge base of low temperature stress change in plants, allowing an evaluation of the uniqueness or generality of Fragaria responses in photosynthetic tissues. Overall, the cold response characteristics of ‘Korona’ are consistent with a moderately cold tolerant plant.

overall_design: Eight weeks old runner-propagated Fragaria × ananassa Duch. ‘Korona’, were grown on fertilized soil (P-Jord; Emmaljunga Torvmull AB) in plug trays (3 x 6 cells) in a greenhouse at 18°C under natural light and long-day conditions. Plants were short-day adapted for 1 week at 12°C under artificial light (fluorescent tubes, ~90 μmol m-2 sec-1) in a conditioning room prior to transfer to a cold storage room at 2°C under artificial light (fluorescent tubes, ~90 μmol m-2 sec-1) and relative humidity at average of 80%. Plant sampling was carried out at times after initiation of the cold treatment. Control samples (0 h) were harvested prior to the transfer to the cold room. Harvested plant material of leaf from 3 plants per time point was pooled, flash-frozen in liquid N2 and stored at -80°C before sample processing.

first: Gage

last: Koehler

first: Jens

last: Rohloff

first: Robert

last: Wilson

first: Joachim

last: Kopka

last: Erban

first: Torfinn

last: Sparstad

first: Jahn

last: Davik

first: Muath

last: Alsheikh

first: Stephen

last: Randall

first: Atle

last: Bones


title: Transcriptional profiling of the plant pathogen Fusarium graminearum on three cereal hosts.

city: Ottawa

first: Linda

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

institute: Agriculture & Agri-Food Canada (AAFC)

summary: Fusarium graminearum gene expression profiles were compared during an early infection time course (1, 2, and 4d post-inoculation) of three monocot hosts (wheat heads, barley heads, and maize developing kernels).

sample_organism:
Hordeum vulgare
Triticum
Triticum aestivum
Zea mays

overall_design: Fusarium-inoculated vs mock-inoculation, 1d, 2d, and 4d post-inoculation, three biological replicates were done for each time point for each host, 2 technical replicates (dye flips) per sample.

first: Anne

last: Johnston

first: Margaret

last: Balcerzak

first: Danielle

last: Schneiderman

first: Ouellet

last: Thérèse


title: Constitutive stringent response restores viability of Bacillus subtilis lacking Structural Maintenance of Chromosome protein

status: Public on Sep 23 2015

city: Jouy-en-Josas

first: Etienne

last: Dervyn

address: domaine de Vilvert

department: Microbiologie

summary: Bacillus subtilis mutants lacking the SMC-ScpAB complex are severely impaired for chromosome condensation and partitioning, DNA repair, and cells are not viable under standard laboratory conditions. We isolated suppressor mutations that restored the capacity of a smc deletion mutant (Δsmc) to grow under standard conditions. These suppressor mutations reduced chromosome segregation defects and abrogated hypersensitivity to gyrase inhibitors of Δsmc. Three suppressor mutations were mapped in genes involved in tRNA aminoacylation and maturation pathways. A transcriptomic survey of isolated suppressor mutations pointed to a potential link between suppression of Δsmc and induction of the stringent response. This link was confirmed by (p)ppGpp quantification which indicated a constitutive induction of the stringent response in multiple suppressor strains. Furthermore, sublethal concentrations of arginine hydroxamate (RHX), a potent inducer of stringent response, restored growth of Δsmc under non permissive conditions. We showed that production of (p)ppGpp alone was sufficient to suppress the thermosensitivity exhibited by the Δsmc mutant. Our findings shed new light on the coordination between chromosome dynamics mediated by SMC-ScpAB and other cellular processes during rapid bacterial growth.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: A 7 array study of the transcriptome profiles of B. subtilis strain 168, CB167 and CB169: ylbM and ywlC mutant strains. Compared to the wild-type strain the mutant strains were used to characterize the effect of the mutation on transcript profiles in order to understand the suppression of the SMC deletion.

first: Camille

last: Benoist

first: Cyprien

last: Guerin

first: Philippe

last: Noirot


title: Expression analysis of Antirrhinum majus inflorescence meristems grown under control and crowding conditions

status: Public on Sep 10 2015

city: Cartagena

first: Marcos

last: Egea-Cortines

address: Edificio I+D+i Plaza del Hospital s/n

department: Instituto de Biotecnología Vegetal

institute: Universidad Politécnica de Cartagena

summary: Investigation of gene expression level changes as a result of crowding growth conditions.

overall_design: A five-chip study using total RNA recovered from samples of inflorescence meristems of Antirrhinum majus cv.165E, grown as single plant per pot (control) and 10 plants per pot (crowded conditions). Each chip measures the expression level of 11,959 ESTs with up to six 60-mer probes per target.

first: Julia

last: Weiss


title: STAT2 and IRF9-dependent IFN-I signaling restores ISRE-mediated transcription and anti-viral activity independent of STAT1 (human)

city: Poznań

first: Hans

last: Bluyssen

address: Umultowska 89

department: Department of Human Molecular Genetics

country: Poland

institute: Faculty of Biology, University of Adam Mickiewicz

summary: Type I Interferons (IFN-I) mediate cellular responses to virus infection. IFN-I induce IFN stimulated gene (ISG) expression by phosphorylating STAT1 and STAT2, and together with interferon regulatory factor (IRF)9, form the transcription complex ISGF3 that binds to the interferon-stimulated response element (ISRE) in ISG promoters. As a component of ISGF3 it is clear that STAT2 plays an essential role in the transcriptional responses to IFN-I with a strong dependence on STAT1. Previously, we showed that STAT2 also forms homodimers that interact with IRF9 (STAT2-IRF9) to activate transcription of ISRE containing ISGs in response to IFN-I. Indeed, evidence is accumulating for the existence of a STAT1-independent IFN-I signaling pathway, where STAT2-IRF9 can substitute the role of ISGF3. Here, we provide further insight in the transcriptional regulation and the biological implications of STAT2-IRF9 dependent IFN-I signaling. In human STAT1 KO cells overexpressing human STAT2 (U3C-STAT2) we observed that in response to IFN-I STAT2 homodimers interact with IRF9 to regulate ISG transcription. The IFN-I-induced phosphorylation profile of STAT2 in U3C-STAT2 was prolonged as compared to WT cells (2fTGH), which corresponded with the expression pattern of OAS2 that also depended on IRF9. Subsequent microarray analysis of IFN-I treated 2fTGH and U3C-STAT2 extended our initial observations and identified more than 60 known antiviral ISGs commonly up-regulated in both cell types. The expression profile of these ISGs was delayed and prolonged in U3C-STAT2 as opposed to the early and transient response in 2fTGH. Moreover, U3C-STAT2 were able to restore an antiviral response upon EMCV and VSV infection that was comparable to the response in 2fTGH. Together, our results strongly suggest that an alternative IFN-I-mediated, STAT2-IRF9 dependent signaling pathway exists that can generate an antiviral response without STAT1 and could be beneficial for example against viruses that directly block STAT1 and impair the formation of ISGF3.

overall_design: Overall 24 samples were analyzed. 2fTGH wild type cells were treated with IFNα  0h, 4h, 8h, 24h in triplicates. HST2-U3C STAT1 KO cells stably overexpressing human STAT2 were treated with IFNα  0h, 4h, 8h, 24h in triplicates. Time point 0h was used as a reference sample.

first: Adam

last: Olejnik

first: Katarzyna

last: Blaszczyk


title: Genome expression profiling identifies host-directed antimicrobial drugs against respiratory infection by nontypable Haemophilus influenzae

city: Pamplona

first: Junkal

last: Garmendia

address: Avda de Pamplona, 123

department: Sanidad Animal

summary: Objectives: Therapies being safe, effective and not vulnerable to develop resistance are highly desirable to counteract bacterial infections. Host-directed therapeutics is an alternative to conventional antibiotics based on perturbing host pathways subverted by pathogens during their life cycle by the use of host-directed drugs to counteract microbial infections. This study sought to identify cellular genes and pathways differentially expressed during airways epithelial infection by nontypable Haemophilus influenzae (NTHi). NTHi is an opportunistic pathogen that is an important cause of exacerbation of chronic obstructive pulmonary disease (COPD). Based on the proposed relationship between NTHi intracellular location and persistence, the antimicrobial potential of a panel of drugs perturbing host pathways used by NTHi to enter epithelial cells was investigated.   Methods: We screened for host genes differentially expressed upon infection by the clinical isolate NTHi375 by analyzing A549 cell whole genome expression profiling, and identified a panel of host target candidates which were pharmacologically modulated. Interfering drugs were tested for their bactericidal effect, cytotoxicity, effect on the interplay NTHi-epithelial cell, and effect on NTHi respiratory infection in vivo, by assessing lung bacterial loads in a murine intranasal infection model.   Results: The sirtuin-1 activator resveratrol showed a bactericidal effect against NTHi; the PDE4 inhibitor rolipram showed therapeutic efficacy by lowering NTHi375 counts both intracellularly and in the lungs of infected mice.  Conclusions: PDE4 inhibition is currently prescribed in COPD; resveratrol is a geroprotector attractive for COPD treatment by preventing lung aging. This work provides evidence for the antimicrobial potential of rolipram and resveratrol against NTHi respiratory infection.

overall_design: Haemophilus influenzae clinical strain NTHi375 induced gene expression in A549 human type II pneumocyte cell line was measured at 2 h post-infection. Non infected cells were used as a control. Four independent experiments were performed for each condition.

first: Begoña

last: Euba

first: Victor

last: Segura


title: STAT2 and IRF9-dependent IFN-I signaling restores ISRE-mediated transcription and anti-viral activity independent of STAT1

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Histone deacetylase inhibitor enhanced salinity stress response

status: Public on Aug 08 2015

city: Nara

first: Kaori

last: Sako

state: Nara

address: 3327-204, Nakamachi

department: Department of Advanced Bioscience

institute: Kindai University

summary: To identify salt-resistant related genes by histone deacetylase inhibitor Ky-2, expression profiles between plants treated with or without Ky-2 under salt stress were analyzed using the custom microarray (GPL20781).

overall_design: Wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on 1/2 MS 0.1 % Agar medium for four days. Then, the plants were administrated to Ky-2 for 24 hours and then treated 100 mM Nacl for two hours. Expression profiles were analyzed using the custom array (GPL20781).

first: Akihiro

last: Matsui

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: Preserved DNA Damage Checkpoint Pathway Protects From Complications in Long-standing Type 1 Diabetes

status: Public on Aug 15 2015

city: Boston

first: Rohit

middle: N

last: Kulkarni

state: MA

address: One Joslin Place

institute: Joslin Diabetes Center

summary:
Gene expression analyses of fibroblasts obtained from healthy controls, Medalist -C patients and Medalist +C patients.
Type 1diabetes (T1D) is associated with late complications, mechanisms underscoring which are poorly understood. We report the derivation of induced pluripotent stem cells (iPSCs) from patients with longstanding T1D (disease duration ≥ 50years) with severe (designated Medalist +C) or absent to mild complications (designated Medalist -C). Disease modeling of iPSCs revealed impairment in growth, reprogramming and differentiation in Medalist +C. Further investigations using genomics and proteomics analyses suggested differential regulation of DNA damage checkpoint proteins favoring protection from cellular apoptosis in Medalist –C. In silico analyses revealed altered expression patterns of DNA damage checkpoint factors among the Medalist groups to be targets of miR200, whose expression was significantly elevated in Medalist +C serum. Notably, neurons differentiated from Medalist +C iPSCs showed enhanced susceptibility to genotoxic stress that worsened upon miR200 over-expression. Furthermore, knockdown of miR200 in Medalist +C fibroblasts and iPSCs rescued checkpoint protein expression and reduced DNA damage response. In summary, we report miR200 regulated DNA damage checkpoint pathway as a potential target for therapeutic intervention for treating complications of diabetes.
Clinical Characteristics of 50 year Medalist Type 1 Diabetes (T1D) patients
Medalist –C:  0/6 with CVD, 5/6 have DN Class 0-IIA, and 6/6 have no to mild NPDR.
Medalist +C: 6/6 with CVD, 5/6 have DN Class IIB or IV, and 4/6 have PDR.
CVD: cardiovascular disease; DN class: diabetic nephropathy class,
PDR: proliferative diabetic retinopathy; NPDR: non proliferative diabetic retinopathy

overall_design: Total RNA was isolated from healthy controls, Medalist -C and Medalist+C fibroblasts in 5.6mM glucose at 24h

first: Manoj

last: Gupta


title: Sphingobium sp. SYK-6 treated with several carbon sources

status: Public on Aug 07 2015

city: Vancouver

first: Hirofumi

last: Hara

state: BC

address: 2350 Health Science Mall

department: Microbilogy and Immunology

institute: University of British Columbia


title: Sphingobium sp. SYK-6 treated with several carbon sources II

summary: Transcriptional profile of RNA extracted from Sphingobium sp. SYK-6 treated with 10 mM dehydrodiconiferyl alcohol (DCA), 10 mM vanillate, or SEMP (10 mM sucrose, 10 mM glutamate, 0.34 mM methionine, and 10 mM proline).

overall_design: Dual channel experiment, RNA from cells treated with DCA or vanillate vs SEMP, independently grown and harvested.

first: Kenji

last: Takahashi

first: Naofumi

last: Kamimura

first: Eiji

last: Masai


title: Microarray Expression profiling of susceptible  (CO-3) and resistant (EC-520061) genotype of tomato in response to Early Blight pathogen after 24hrs of inoculation

status: Public on Jul 29 2015

city: VARANASI

first: PRITI

last: UPADHYAY

address: VARANASI

department: GENETICS AND PLANT BREEDING

country: India

institute: BANARAS HINDU UNIVERSITY

summary:
A comparative study ware made to know the Early Blight resistance mechanism between resistant and susceptible plants at vegetative stage.
Transcriptional changes during compatible and resistant reaction between A. solani and tomato genotypes have been identified using Affymetrix tomato gene chips. Results were confirmed by reverse transcription-polymerase chain reaction with the samples collected after 24hrs of inoculation from inoculated and control susceptible and resistant genotypes. The number of up and down regulated genes in three different combinations of treatments i.e. Early Blight Resistant Treated and Control (EBTT and EBTC) and Early Blight Suceptible Treated and Control (EBST and EBSC)  has observed and compared.  In EBST vs. EBSC condition, 3478 genes are up regulated and 2663 are down regulated. Similarly when analysis is done between EBST and EBRT, 2475 genes are up regulated and 3662 are down regulated. Total 3442 genes are up regulated and 2695 genes are found to be down regulated in resistant line of tomato for early blight when the analysis is done for EBRT Vs. EBRC. These genes, that are induced in the resistant genotype EC-520061(Solanum habrochaites , wild)  of  tomato, after Alternaria solani infection, have been classified in to following categories, response to stress, cellular component,  Metabolic activity, regulation of transcription,  regulation of translation, and few were unknown. Data from this study are a resource for understanding the mechanism, which works for resistance against pathogen of early blight in tomato, which is critical and will be useful in improving this trait through transgenic approach or gene silencing.

sample_organism:
Solanum lycopersicum
Solanum habrochaites

overall_design: Tomato plants were exposed to A. solani spores and after 24 hrs (at the stage of penetration of tissues with fungal hyphae) samples were collected from both susceptible and resistant genotypes for RNA extraction and hybridization on Affymetrix chips. To study the molecular mechanism of biotic stress resistance, transcripts of both the genotypes were compared in response to A. solani.

first: Upadhyay

last: Priti

first: Rai

last: Ashutosh

first: Singh

last: Major

first: Kumar

last: Rajesh

first: Sinha

last: Brajesh


title: Integrated analyses of zebrafish miRNA and mRNA expression profiles identify miR-29b and miR-223 as potential regulators of optic nerve regeneration

status: Public on Jun 26 2015

city: Perth

first: Kim

middle: Warwick

last: Carter

state: Western Australia

address: 100 Roberts Road, Subiaco

country: Australia

institute: Telethon Kids Institute

summary: We used microarrays to analyse expression profiles of zebrafish retina after optic nerve crush to identify potential regulatory mechanisms that underpin central nerve regeneration

overall_design: Total RNA extracted from 4 samples (pooling 4 animals) of Zebrafish retinae after performing optic nerve crush (at day 3 post crush) vs 4 samples (pooling 4 animals) of control (unoperated) Zebrafish retinae

first: P

middle: I

last: Fuller-Carter

first: K

middle: W

first: D

last: Anderson

first: A

middle: R

last: Harvey

last: Giles

first: J

last: Rodger


title: Sphingobium sp. SYK-6 treated with several carbon sources I

summary: Transcriptional profile of RNA extracted from Sphingobium sp. SYK-6 treated with 10 mM dehydrodiconiferyl alcohol (DCA), 10 mM vanillate, or SEMP (10 mM sucrose, 10 mM glutamate, 0.34 mM methionine, and 10 mM proline) comparing labeled SYK-6 genomic DNA.

overall_design: Dual channel experiment, RNA from cells treated with DCA, vanillate, or SEMP vs. genomic DNA. 3 control of genomic DNA, independently grown and harvested.


title: Clostridium thermocellum DSM 1313 Transcriptional Responses to Redox Perturbation

city: Oak Ridge

first: Kyle

last: Sander

state: TN

address: 1 Bethel Valley Road, MS 6038

department: Biosciences

institute: University of Tennessee/Oak Ridge National Laboratory

summary: Clostridium thermocellum is a promising CBP candidate organism capable of directly converting lignocellulosic biomass to ethanol.  Low yields, productivities and growth inhibition prevent industrial deployment of this organism for commodity fuel production.  Symptoms of potential redox imbalance such as incomplete substrate utilization, and fermentation products characteristic of overflow metabolism, have been observed during growth.  This perceived redox imbalance may be in part responsible for the mentioned bioproductivity limitations.  Toward better understanding the redox metabolism of C. thermocellum, we analyzed gene expression, using microarrays, during addition of two stress chemicals (methyl viologen and hydrogen peroxide) which we observed to change fermentation redox potential.

overall_design: High quality RNA was extracted from C. thermocellum grown on cellobiose in chemostat culture and exposed, separately, to methyl viologen and hydrogen peroxide. Transcriptome profiles were obtained at seven time points during actively growing fermentations, 3 minutes, 15 minutes, 35 minutes, 7 hours, 14 hours, 50 hours, and 60 hours after beginning exposure to each stressor.  Exposure treatments were carried out in duplicate and reference/untreated samples were taken before and between treatments, after flushing of stressor chemicals and re-equilibration of growth conditions.

first: Charlotte

last: Wilson

first: Miguel

last: Rodrigues Jr.

first: Dawn

last: Klingeman

first: Brian

last: Davison

first: Steven

middle: D

last: Brown


title: Microbial and Functional Diversity within the Phyllosphere of Espeletia sp. in Andean High Mountain Ecosystems

status: Public on Jul 09 2015

city: Bogota

first: Carlos

middle: Alexander

last: Ruiz Perez

state: CUNDINAMARCA

country: Colombia

institute: Corporacion CorpoGen

summary: Functional profiles predicted based on taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacity based on plant location. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Sixteen samples analyzed.

first: Maria

last: Zambrano

first: Silvia

last: Restrepo


title: miR-200c Targets CDK2 and Suppresses Tumorigenesis in Renal Cell Carcinoma

status: Public on Jul 25 2015

city: wuhan

first: xuegang

last: Wang

address: 1277 Jiefang Avenue

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan

summary: MicroRNAs (miRNAs) expression profiles are widely investigated in the major cancers, but their specific roles and functions in cancers have not yet to be fully elucidated. We investigated expression profiles of miRNAs in clear cell renal cell carcinomas (ccRCCs) and in matched normal kidney tissues (NCTs) by using a miRNAs microarray platform which covers a total of 851 human miRNAs.

overall_design: Tumor tissue samples were immediately snap-frozen in liquid nitrogen after surgery, and then stored in a deep freezer at -80°C. Total RNA was extracted from 5 ccRCC tissues and paired NCTs and expression profiles of miRNAs were screened by using a miRNA microarray platform.

first: Xuegang

first: Xiaoping

last: Zhang


title: Genome map of SND1 binding sites by ChIP-chip analysis in human HepG2 cells under inflammatory conditions.

status: Public on Jul 31 2015

city: Leioa

first: Enara

last: Arretxe

address: Sarriena

department: Phisiology

institute: University of the Basque Country

summary: Profiling of promoter occupancy by SND1 coactivator in human hepatoma cells. Control  and TNFα-treated HepG2 cells are immunoprecipitated with anti-SND1 antibody and input and immunoprecipitated material were hybridized in an Agilent human promoter microarray

overall_design: Two-condition experiment. Biological replicates: 3 control replicates, 3 TNFα-treated replicates. Input vs. Immunoprecipitated material

first: María

last: Martínez


title: TRPM7 maintains mesenchymal phenotype of breast cancer cells by tensional regulation of SOX4 (SOX4 shRNA)

status: Public on Jun 16 2015

city: Nijmegen

first: Arthur

last: Kuipers

address: PO Box 9101

country: Netherlands

institute: Radboudumc

summary:
Analysis of the effect of shRNA-mediated knockdown of SOX4 on global gene expression levels in MDA-MB-231 human breast cancer cells.
Results were used for the identification of overlapping up- and downregulated genes in TRPM7 + SOX4 shRNA MDA-MB-231 cells

overall_design: Total RNA isolated from MDA-MB-231 breast cancer cells transduced with a scrambled shRNA  (shCntrl) or SOX4 shRNA (shSOX4#1)

first: Jeroen

last: Middelbeek

first: Geert

last: Poelmans

first: Jeffrey

last: Klarenbeek

first: Kees

last: Jalink

first: Frank

last: van Leeuwen


title: The role of interleukin-1 beta in the pathophysiology of Schnitzler’s syndrome

status: Public on Aug 01 2015

first: Heleen

last: de Koning

state: Gelderland

address: Geert Grooteplein-Zuid 10

summary: Schnitzler’s syndrome (SchS) is a disabling autoinflammatory disorder, characterized by chronic urticaria a chronic urticarial rash, an M-protein, arthralgia, and other signs of systemic inflammation. Anti-interleukin-1 (IL-1) beta antibodies are highly effective, but the pathophysiology is still largely unknown. Here we studied the effect of in-vivo IL-1 inhibition on serum markers of inflammation and cellular immune responses.

overall_design: Transcriptome analysis of RNA from PBMCs from three patients with Schnitzler’s syndrome and three matched controls. Patient samples were drawn during symptomatic disease, anakinra and canakinumab treatment.

first: Joost

last: Schalkwijk

first: Monique

last: Stoffels

first: Johanna

last: Jongekrijg

first: Joannes

middle: F

last: Jacobs

first: Eugène

middle: T

last: Verwiel

first: Hans

last: Koenen

last: Preijers

first: Dirk

last: Holzinger

first: Irma

last: Joosten

first: Jos

last: van der Meer

first: Anna

last: Simon


title: TRPM7 maintains mesenchymal phenotype of breast cancer cells by tensional regulation of SOX4

status: Public on Jun 13 2015

first: Arthur

last: Kuipers


title: Genome-wide perturbations by miRNA map onto functional cancer pathways identifying regulators of chromatin modifiers

status: Public on Mar 31 2015

city: Houston

first: Prahlad

middle: T.

last: Ram

address: 7435 Fannin St.

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

overall_design: Total RNA obtained from cancer cell lines transfected with miR-365-3p for 24 hours compared to controls.

first: Tyler

last: Moss


title: A large germline alteration affecting MAX and FUT8, causing familial bilateral malignant pheochromocytoma and renal oncocytoma

status: Public on May 13 2015

city: Rotterdam

first: Esther

last: Korpershoek

address: Wytemaweg 80

department: Pathology

institute: Erasmus MC University Medical Center Rotterdam

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

summary: Familial pheochromocytoma (PCC) has been associated with germline mutations in 14 genes. Here we investigated three siblings, who presented with (metastatic) bilateral pheochromocytomas, renal oncocytoma, and erythrocytosis. By SNP-array on one patient’s germline DNA a large complex genomic alteration was identified  encompassing the intragenic and promoter regions of Myc-Associated Factor X (MAX) and alpha-(1,6)-fucosyltransferase (FUT8). The alteration was confirmed in all patients, as well as loss of the wild type MAX and FUT8 alleles and corresponding loss of protein expression. Uniparental disomy of chromosome 14q, previously demonstrated as a hallmark for MAX-related PCC, was also shown in the index patient by SNP-array. Our results indicate that large genomic deletions of MAX should be considered in familial and bilateral PCC with prior negative testing for gene mutations. In addition, MAX appears to be a new tumor suppressor gene for renal oncocytomas.

overall_design: SNP array was performed for 2 samples: 1 tumor DNA sample and 1 corresponding germline DNA sample


title: Transcriptional correlates of FOXP3 expression in suppressive and non-suppressive primary human Treg cell clones.

status: Public on May 06 2015

city: Montreal

first: Eva

last: d'Hennezel

state: Quebec

address: 1650 Cedar avenue

department: Microbiology and Immunology

institute: McGill University

summary: Analysis of the transcriptional correlates of FOXP3 expression in suppressive and non-suppressive primary human Treg cell clones. Individual CD4+CD25High or Cd4+CD25- T cells were isolated from human PBMCs and expanded in vitro. After 3 weeks of expansion, individual clones were analysed for FOXP3 expression and in vitro suppressive activity against freshly sorted allogeneic effector T cells. This study analyses the total RNA isolated from FOXP3+ clones with suppressive potency to their non-suppressive counterparts. The resutls of this study should provide insights into the molecular pathways linking FOXP3 expression to distinct aspects of Treg phenotype and function.

overall_design: Total RNA obtained from individual clones of primary human regulatory and effector CD4+T cells.

first: Khalid

last: Bin Dhuban

first: Ola

last: Larsson

first: Ciriaco

last: Piccirillo


title: Difference of microRNA expressions between a mouse model of NASH(MCD diet) and normal mouse.

status: Public on Mar 01 2015

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The microRNAs expression was markedly altered with the MCD diet.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 1135 mouse microRNA probes in liver tissue that were fed MCD diet.

first: Akiko

last: Katsura

first: Tsutomu

last: Masaki


title: TRPM7 maintains mesenchymal phenotype of breast cancer cells by tensional regulation of SOX4 (TRPM7 shRNA)

summary:
Analysis of the effect of shRNA-mediated knockdown of TRPM7 on gene expression levels in MDA-MB-231 human breast cancer cells.
Results were used for the identification of so-called epithelial-mesenchymal transcription factors that were affected by TRPM7 knockdown and for the analysis of overlapping up- and downregulated genes in shT7#1 + shSOX4#1 MDA-MB-231 cells

overall_design: Total RNA isolated from MDA-MB-231 breast cancer cells transduced with a scrambled shRNA  (shCntrl) or TRPM7 shRNA (shT7#1)

first: Jeroen

last: Middelbeek

first: Geert

last: Poelmans

first: Jeffrey

last: Klarenbeek

first: Kees

last: Jalink

first: Frank

last: van Leeuwen


title: Gene expression data from control and REPTOR (=CG13624) KO male adults

status: Public on Apr 30 2015

city: Heidelberg

first: Aurelio

last: Teleman

address: Im Neuenheimer Feld 580

institute: German Cancer Research Center (DKFZ)

summary:
The aim was to identify genes whose transcription is induced or repressed by REPTOR (=CG13624) KO in Drosophila melanogaster male adults.
Data are part of the manuscript REPTOR and REPTOR-BP regulate organismal metabolism and transcription downstream of mTORC1

overall_design: 2 biological replicates from 2 conditions: Control adult males / REPTOR KO adult males ; 4 samples

first: Marcel

last: Tiebe

first: Marilena

last: Lutz

first: Adriana

last: De La Garza

first: Tina

last: Buechling

first: Michael

last: Boutros


title: Deletion of the gene family of small chlorophyll-binding proteins (ScpABCDE) offsets C/N homeostasis in synechocystis PCC 6803

status: Public on Mar 30 2015

city: Sydney

first: Miguel

last: Hernández-Prieto

state: NSW

address: Macleay Building A12

department: School of life and environmental sciences

institute: University of Sydney

summary: Small CAB-like proteins (SCPs) are single-helix light-harvesting-like proteins found in all organisms performing oxygenic photosynthesis. We investigated the function of these stress-induced proteins in the cyanobacterium Synechocystis sp. PCC 6803 by comparing a strain, which expresses SCPs constitutively, with a mutant lacking all five SCPs. In the absence of SCPs, cells were larger, and showed irregular thylakoid structure and cell-surfaces. Deletion of scp genes strongly affected the carbon-nitrogen balance, causing accumulation of carbohydrates and a decrease in N-rich compounds (proteins and chlorophyll a). Data from transcriptomic and metabolomic experiments demonstrated that SCPs mediated stabilization of chlorophyll a under stress conditions is crucial to maintain the C/N balance. SCPs diminished the formation of reactive oxygen species, preventing cellular damage by adjusting the de-novo production of chlorophyll a to demand levels. Lack of SCP expression under stress conditions had a large impact on the metabolism of the entire cell.

overall_design: Synechocystis 6803 PSI-less (Shen et al 1993) and PSI-less/ScpABCDE- (Xu et al 2004) mutants were cultivated at 30°C at a light intensity of 4–5 μmol photons m–2 s–1 in BG-11 growth medium (Rippka et al 1979) supplemented with 10 mM glucose. Cells (40–50 ml) from both control and the mutant cultures were collected at mid-log phase by rapid filtration (Pall Supor 800 Filter, 0.8 mm) and total RNA extracted after Pinto et al. (Pinto et al 2009). Single-stranded cDNA preparation, labelling, and hybridization onto the microarray slides were performed after Eisenhut et al. (2007). The microarray slides were scanned with an Agilent Microarray Scanner (model G2505B) with default settings.


title: Gene expression data from control and REPTOR KO larvae after 6h rapamycin treatment

summary:
The first aim was to identify genes whose transcription is induced by rapamycin feeding in Drosophila larvae.
Secondly, the goal was to find out which contribution the transcription factor REPTOR (=CG13624) has to the observed changes in expression. We thus compared gene epxression between rapamycin fed and control fed larvae in wild type larvae and in REPTOR KO larvae.

overall_design: 3 biological replicates from 4 conditions: control larvae plus/miuns rapamycin, KO larvae plus/minus rapamycin; overall 12 samples


title: Leukocyte gene expression variation as a function of psychological well-being II

status: Public on Mar 28 2015

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary: Individual differences in basal leukocyte gene expression profiles as a function of hedonic and eudaimonic well-being, and psychological and social sub-dimensions of eudaimonic well-being.

overall_design: Gene expression profiling was carried out on peripheral blood mononuclear cell RNA samples collected from 122 healthy adults measured for hedonic and eudaimonic dimensions of well-being using the Short Flourishing Scale (Keyes, C (2014).  The Mental Health Continuum-Short Form (MHC-SF) for adults).  Higher values of the hedonic well-being scale indicate greater levels of positive affect, higher values of eudaimonic well-being scale indicate greater experience of purpose and meaning in life,  higher values of social well-being scale indicate greater experience of social well-being in life,  higher values of psychological well-being scale indicate greater experience of psychological well-being in life, greater TotalMHCSF scores indicate greater experience of all forms of well-being measured by the MHC-SF, the FlourishGroup indicates idividuals showing flourishing mental health as defined by the MHC-SF scoring instructions referenced above, greater BrownPsychological scores indicate greater experience of psychological well-being as measured by the MHC-SF with an alternative scoring, and greater BrownSocial scores indicate greater experience of social well-being as measured by the MHC-SF with an alternative scoring.


title: Leukocyte gene expression variation as a function of chronic caregiving stress

summary:
This study explored how chronic stress influences the activity of signaling pathways that regulate inflammation in the human monocyte transcriptome. The sample consisted of 33 adults caring for a family member with glioblastoma, a terminal brain cancer, and 47 control subjects whose lives were free of major stressors. The subjects were assessed on four occasions across an eight-month period. Relative to controls, caregivers’ monocytes showed increased expression of genes bearing response elements for nuclear-factor kappa B, a key pro-inflammatory transcription factor in monocytes. Simultaneously, caregivers showed reduced expression of genes with response elements for the glucocorticoid receptor, a transcription factor that conveys anti-inflammatory signals to monocytes. These transcriptional disparities were not attributable to demographic or behavioral confounds. They also were not attributable to differences in diurnal cortisol output, or the abundance of glucocorticoid receptor expressed by monocytes. In ex vivo studies of monocytes stimulated with the bacterial product lipopolysaccharide, caregivers showed increased production of the pro-inflammatory cytokine interleukin-6, and were less sensitive to cortisol-mediated inhibition of this response. These findings suggest a scenario wherein chronic stressors engender functional changes that hamper monocytes’ capacity to transduce cortisol’s anti-inflammatory signals. These changes occur in parallel with, and perhaps enable, greater inflammatory signaling via nuclear-factor kappa B. The resulting inflammatory milieu could serve as a pathogenic mechanism through which chronic stressors like caregiving accentuate vulnerability to later health problems.
series type: Risk prediction

overall_design:
Individual differences in basal leukocyte gene expression profiles as a function of chronic caregiving stress
Characteristics included in statistical analyses of gene expression data are provided in each sample records.
Please note that educational attainment is scored as following; 0=less than high school, 1=high school diploma or equivalent, 2=associate's degree, 3=bachelor's degree, 4=masters degree, 5=doctoral degree


title: Gene expression after rapamycin treatment in control, REPTOR or REPTOR-BP knockdown S2 cells

summary:
The first aim was to identify genes whose transcription is induced by rapamycin feeding in Drosophila S2 cells.
Secondly, the goal was to find out which contribution the transcription factors REPTOR (=CG13624) and REPTOR-BP (REPTOR-binding partner, =CG18619) has to the observed changes in expression. We thus compared gene epxression between rapamycin and control treated S2 cells in GFP, REPTOR or REPTOR-BP knockdown cells.

overall_design: 3 biological replicates from control knockdown plus/minus rapamycin and REPTOR knockdown plus/minus rapamycin; 2 biological replicates from REPTOR-BP knockdown cells plus/minus rapamycin; together those are 16 samples


title: Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions II

status: Public on Mar 29 2015

city: La Jolla

first: Francesca

last: Boscolo

address: 9500 Gilman Drive

department: Reproductive Medicine

institute: UCSD

summary: The self-renewal and differentiation capacities of human pluripotent stem cells (hPSCs) make them good sources of cells for cell transplantation therapy, drug development, and studies of cellular differentiation and development.  However, the large numbers of cells necessary for many of these applications require extensive expansion of hPSC cultures, a process that has been associated with genetic and epigenetic alterations.  We have performed a combinatorial study on both hESCs and hiPSCs to compare the effects of enzymatic vs. mechanical passaging, and feeder-free vs. mouse embryonic fibroblast feeder substrate, to on the genetic and epigenetic stability and the phenotypic characteristics of hPSCs.  In extensive experiments in hEScs involving over 100 continuous passages, , we observed that both enzymatic passaging and feeder-free culture were associated with genetic instability, higher cell proliferation, and persistence of OCT4-positive cells in teratomas, with enzymatic passaging having the stronger effect. In all combinations of culture conditions except for mechanical passaging on feeder layers, we noted recurrent deletions in the genomic region containing the tumor suppressor gene TP53, which was associated with decreased mRNA expression of TP53, as well as alterations in the expression of several downstream genes consistent with a decrease in the activity of the TP53 pathway.  Among the hESC cultures, we also observedculture-dependent variations in global gene expression and DNA methylation.  Verification of the negative effects of enzymatic passaging and feeder-free conditions was performed in hiPSC cultures. Our results highlight the need for careful assessment of effects of culture conditions on cells intended for clinical therapies.

overall_design: Three independent hiPSC clones reprogrammed from human fetal dermal fibroblasts: HDF51iPS1, HDF51iPS7, and HDF51iPS11.

first: Louise

last: Laurent


title: Study of microRNA associated with metformin treatment in a mouse model of NASH(MCD)

first: Satoshi

last: Kondo

summary: The microRNAs expression was altered with the treatment of metformin in vivo and several microRNAs induced by metformin also may contribute to suppressed of NASH.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 1135 mouse microRNA probes in liver tissue in vivo that were treated with and without metformin.

first: Akiko

last: Katsura


title: Gene expression profile of A549 Circulating Tumor Cells from 4D Model.

status: Public on Mar 12 2015

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: CTCs in cancer patients are thought to be responsible for metastasis. Currently, there is no ex vivo model that can isolate this group of cells. We have developed an ex vivo 4D lung cancer model that forms perfusable tumor nodules and form CTCs. Gene array analyses show 2504 differentially expressed genes when comparing CTCs from the 4D model seeded with A549 cells to the same cells grown on a petri dish (2D).

overall_design: We compared the gene expression profile (Human OneArray v5 chip) of A549 cells, human lung cancer cell line, grown on petri dish (2D) and same cells circulating as tumor cells in our ex vivo model (4D/CTC).

first: Min

last: Kim

first: Dhruva

last: Mishra

first: Yiqun

last: Zhang


title: Leukocyte gene expression variation as a function of perceived family stress and psychological well-being

summary: Individual differences in basal leukocyte gene expression profiles as a function of child's and parent's perception of family stress, and as a function of parent's psychological well-being.

overall_design:
Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from 273 individuals (129 parent:child pairs + 15 parent-or-child) who were also assessed on their perceptions of family stress (both parent's and child's perception). Each dyad is labeled by a case ID, with p suffix indicating parent's gene expression profile and c suffix indicating child's gene expression profile.  Variations in gene expression are analyzed as a function of both parent's perception of family stress and child's perception of family stress (using UCLA Life Stress Interview, as previously described: Hammen C (1991) Generation of stress in the course of unipolar depression. J Abnorm Psychol 100:555-561; Adrian C, Hammen C (1993) Stress Exposure and Stress Generation in Children of Depressed Mothers. Journal of Consulting and Clinical Psychology 61:354-359; Rudolph KD, Hammen C (1999) Age and gender as determinants of stress exposure, generation, and reactions in youngsters: A transactional perspective. Child Development 70:660-677).  Higher values indicate greater levels of subjectively perceived family stress.  Additional data are available for 107 parents who completed all 6 subscales of the Psychological Well-Being (PWB) Scale (Ryff CD (1989) Happiness is everything, or is it?  Explorations on the meaning of psychological well-being. J. Pers Soc. Psychol 57: 1069-1081), resulting in scores for PWB_Total (average score across all 6 subscales) as well as scores for subscales measuring Purpose in Life (PWB_Purpose), Environmental Mastery (PWB_Environmental_Mastery), Self-Acceptance (PWB_Self_Accept), Autonomy (PWB_Autonomy), Personal Growth (PWB_Growth), Positive Relations with Others (PWB_Relationship).  Higher scores indicate greater psychological well being.  Also available for those individuals are measures of age (years), male gender (0/1), ethnic group (1=White, 2=Chinese, 3=Indian, 4=Other Asian, 5=Other Ethnicity), Body Mass Index (kg/m^2), heavy alcohol consumption history (0/1), smoking history (0/1), and abundance of 8 mRNA transcripts indicating the relative prevalence of major leukocyte subsets (CD3E, CD3D, CD19, CD4, CD8A, FCGR3A, NCAM1, CD14).
key word: Risk prediction


title: REPTOR and REPTOR-BP regulate organismal metabolism and transcription downstream of mTORC1

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

overall_design: Refer to individual Series


title: Local regulation of the Srs2 helicase by the SUMO-like domain protein Esc2 promotes recombination at sites of stalled replication

status: Public on Feb 16 2015

city: Milan

first: Madhusoodanan

last: Urulangodi

state: Milan

address: Via Adamello 16

country: Italy

institute: IFOM

summary: Accurate completion of replication relies on the ability of cells to activate error-free recombination-mediated DNA damage-bypass at sites of perturbed replication. However, as anti-recombinase activities are also recruited to replication forks, how recombination-mediated damage-bypass is enabled at replication stress sites remained puzzling. Here we uncovered that the conserved SUMO-like domains-containing Saccharomyces cerevisiae protein, Esc2, facilitates recombination-mediated DNA damage tolerance by allowing optimal recruitment of the Rad51 recombinase specifically at sites of perturbed replication. Mechanistically, Esc2 binds stalled replication forks and counteracts the anti-recombinase Srs2 helicase via a two-faceted mechanism involving chromatin recruitment and turnover of Srs2. Importantly, point mutations in the SUMO-like domains of Esc2 that reduce its interaction with Srs2 cause sub-optimal levels of Rad51 recruitment at damaged replication forks. In conclusion, our results reveal how recombination-mediated DNA damage tolerance is locally enabled at sites of replication stress, while globally prevented at undamaged replicating chromosomes.

overall_design: One INPUT (SUP) with the corresponding IP samples for each ChIP on chip. The following samples are processed. Elg1-FLAG, esc2Δ Elg1-FLAG, Rad51, esc2ΔRad51, Esc2-Myc, Esc2Δ154_198_Myc, Pol3-Myc, and Brdu. Cells were grown in 200 ml of YPD media at 25°C in 1L falsk for a density of 1.2×10^7 cells/ml. G1 synchronization was performed by α−factor treatment (2 μg/ml) for 150 minutes. Cells were pelleted and released in media containing 0.2 M HU at 25°C for 30 (Rad51), 60 min (Elg1-FLAG, Esc2-Myc, Esc2Δ154_198-Myc or 90 min (Pol3-Myc and Brdu) and fixed with 1% formaldehyde for 30 min or 120 (as indicated) min at room temperature. Proteins ChIP-chip analyses were carried out as described (Bermejo R, Katou YM, Shirahige K, Foiani M. ChIP-on-chip analysis of DNA topoisomerases. Methods Mol Biol. 2009;582:103-18). Labelled probes were hybridized to Affymetrix S. cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

first: Marek

last: Sebesta

first: Demis

last: Menolfi

first: Barnabas

last: Szakal

first: Julie

last: Sollier

first: Alexandra

last: Sisakova

first: Lumir

last: Krejci

first: Dana

last: Branzei


title: Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals [Expression 1]

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Microbiologie and Infectiologie

institute: Université de Sherbrooke Centre of Excellence in RNA Biology

type: Expression profiling by genome tiling array

summary: Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes and their impact on RNA expression is linked to growth conditions. Together the data suggest that stability of the yeast transcriptome is regulated by malleable RNA degradation signals that permit dynamic response to changes in growth conditions.

overall_design: WT, rnt1 delta and rrp6 delta strains where grown independently and analyzed by Affymetrix yeast tiling microarray analysis

first: Jules

last: Gagnon

first: Mathieu

last: Lavoie

last: Catala

first: Francis

last: Malenfant


title: Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals [Expression 2]

summary: Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes and their impact on RNA expression is linked to growth conditions. Together the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions.

overall_design: Total RNA and whole cell extract from rnt1d strain was divided in two samples. One sample was treated with purified Rnt1p. The other was only incubated with buffer. The two samples were then treated with recombinant Xrn1p.


title: Real Time PCR analysis of T helper cells

status: Public on Feb 03 2015

city: Lodz

first: Marcin

middle: P

last: Mycko

address: Kopcinskiego 22

department: Department of Neurology

institute: Medical University of Lodz

summary:
Murine lymphocytes T helper cells were obtained from spleen of C57Bl/6 mice and miR-155 deficient mice strains that have been immunised with MOG peptide 35-55 in complete Freunds adiuvant 12 days prior.
Subsequently cells were stimulated for 72 hours with MOG peptide 35-55 or left unstimulated followed by T helper cell sorting using magnetic beads and RNA isolation.

overall_design: qPCR gene expression profiling. Cells from three individual mice of the same genotype were pooled and treated separately as indicated in the summary. Equal amount total RNA from each mice was pooled prior to gene expression analysis.

first: Maria

last: Cichalewska


title: Leukocyte gene expression variation as a function of Big 5 dimensions of human personality

status: Public on Jan 28 2015

first: Steve

last: Cole

summary: Individual differences in basal leukocyte gene expression profiles as a function of Big 5 personality dimensions

overall_design:
Gene expression profiling was carried out on peripheral blood mononuclear cell RNA samples collected from 119 healthy adults measured for the 5 major dimensions of human personality (Neuroticism, Extraversion, Openness, Agreeableness, Conscientiousness) using the NEO-FFI 60-item personality inventory.  Personality measures are z-score standardized.  Analyses control for major demographic characteristics (age, sex, Caucasian vs Non-Caucasian race) as well as Body Mass Index (BMI), smoking (CigDay), alcohol consumption (AlcDay), and physical activity (ExerDay, hours per day).  Additional secondary analyses controlled for the presence of minor physical symptoms (MinorSymptom, e.g.,hayfever, headache), medication use (BirthControl, Antidepressant, OtherMedication), and negative affective states (NegativeAffect, standardized values of PANAS Negative Affect scale).

Experiment type: Risk prediction


title: A Human Model of Cerebral Amyloid Angiopathy Using Neural Crest-Derived Vascular Smooth Muscle Cells

status: Public on Jan 21 2015

city: Singapore

first: Jingxian

last: Zhang

state: Singpaore

address: 61 Biopolis Drive Proteos

department: IMCB

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore

summary: There is a growing recognition of cerebrovascular contribution to neurodegenerative diseases. Cerebral amyloid angiopathy (CAA), characterised by amyloid-beta (Aβ) deposits in the walls of intracerebral and leptomeningeal arteries, is evident in a majority of Alzheimer’s disease patients and aged people. Here, we leverage on human pluripotent stem cells to generate vascular smooth muscle cells (SMCs) from neural crest progenitors, recapitulating brain vasculature-specific attributes in Aβ metabolism. We confirm that the lipoprotein receptor, LRP1, functions in our neural crest-derived SMCs to mediate Aβ uptake and intracellular proteasomal degradation. Hypoxia significantly compromises the ability of SMCs in Aβ clearance by suppressing LRP1 expression. This enables us to develop an assay of Aβ uptake using the neural crest-derived SMCs with hypoxia as a stress paradigm. We then tested several vascular protective compounds in a high throughput format, demonstrating the value of stem cell-based phenotypic screening for novel CAA therapeutics and drug repurposing.

overall_design: We adopted our previous SMC differentiation protocol (Cheung et al., 2012) to differentiate this intermediate neural crest population using platelet-derived growth factor BB (PDGF-BB, 10 ng/ml) and transforming growth factor-beta 1 (TGF-β1, 2ng/ml) for another 12 days. The resultant neural crest-derived SMCs (NCSMC) were then characterised in comparison to neuroectoderm-derived SMCs (NESMC) (Cheung et al., 2012) and positive control, human brain vascular SMCs (BVSMC).

first: Christine

last: Cheung

first: J


title: Effect of mir-210 over-expression on the miRNAome of human umbilical vein endothelial cells

status: Public on Jan 01 2015

first: Fabio

last: Martelli

address: via morandi 30

institute: IRCCS-Policlinico San Donato

summary: MicroRNAs (miRNAs) are small non-protein-coding RNAs that are incorporated into the RNA-induced silencing complex (RISC) and inhibit gene expression by regulating the stability and/or the translational efficiency of target mRNAs. miR-210 can be considered a master miRNA of hypoxic response and is currently regarded as a promising novel non-invasive tumor hypoxia marker. The targets identified to date indicate that miR-210 plays a role in cell cycle regulation, differentiation, mitochondrial metabolism repression, DNA repair and apoptosis. In order to identify miRNAs sub-sequentely modulated by miR-210, miRNA expression profiles of human umbilical vein endothelial cells (HUVEC) over-expressing miR-210 were generated, allowing the identification of miRNAs modulated upon miR-210 up-regulation.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: HUVEC over-expressing pre-miR-210 or a scramble sequence were generated by retroviral infection, yielding a selected population that expressed mature miR-210 levels comparable with those observed in hypoxic cells. miRNA expression profiles were then measured and miRNAs modulated upon miR-210 up-regulation were identified. This Sample represents four hybridizations - one of which was a dye-swap.

first: P

last: Fasanaro

first: C

last: Voellenkle

first: F


title: TRPM7 maintains progenitor-like features of neuroblastoma cells

status: Public on Dec 10 2014

first: Jeroen

last: Middelbeek

address: POBOX 9101

department: Pediatric Oncology

summary: Analysis of the effect of shRNA-mediated knockdown of TRPM7 on gene expression levels in SH-SY5Y and SH-EP2 human neuroblastoma cells. Results were used for the identification of neural-crest-associated transcription factors that were affected by TRPM7 knockdown.

overall_design: Total RNA isolated from SH-EP2 and SH-SY5Y human neuroblastoma cells transduced with a scrambled shRNA (control) or TRPM7 shRNA, experiment performed in duplicate.

first: Daan

last: Visser

first: Linda

last: Henneman

first: Alwin

last: Kamermans

first: Arthur

last: Kuipers

first: Peter

middle: M

last: Hoogerbrugge

first: Kees

last: Jalink

first: Frank

last: van Leeuwen


title: Comparative Genome-wide expression profiling of ADLD whole blood and fibroblasts cell lines.

status: Public on Jan 29 2015

city: Bologna

first: Sabina

last: Capellari

address: via Altura, 3

department: Dibinem and UOC clinica Neurologica

institute: University of Bologna And IRCCS ISNB

summary: Adult-onset autosomal dominant leukodystrophy (ADLD) is a slowly progressive neurological disorder characterized by autonomic dysfunction, followed by cerebellar and pyramidal features. ADLD is caused by duplication of the lamin B1 gene (LMNB1), which leads to its increased expression. The molecular pathways involved in the disease are still poorly understood. Hence, we analyzed global gene expression in fibroblasts and whole blood of LMNB1 duplication carriers and used Gene Set Enrichment Analysis (GSEA) to explore their gene signatures. We found that LMNB1 duplication is associated with dysregulation of genes involved in the immune system, neuronal and skeletal development. Genes with an altered transcriptional profile clustered in specific genomic regions.

overall_design: To identify altered pathways in ADLD, we performed a whole genome expression profiling on fibroblasts cell lines derived from 4 ADLD, 3 controls siblings, 2 age match controls, 2 uninvestigated samples; and from 4 ADLD whole blood, 8 controls siblings and 1 uninvestigated sample.

first: Anna

last: Stella


title: TRANSCRIPTOME MODIFICATIONS IN HUMAN GINGIVAL FIBROBLASTS EXPOSED TO 2-HYDROXYETHYL-METHACRYLATE (HEMA)

status: Public on Dec 15 2014

city: Chieti

first: Valentina

last: Gatta

state: Abruzzo

address: Via Colle Dell'Ara

department: Department of Psychological SciencesDepartment of Psychological Sciences

institute: University G.d'Annunzio

summary:
Objective: 2-Hydroxyethyl methacrylate (HEMA), one of the most common components of tooth filling materials, could diffuse throughout dentine, and in gingival and pulp cells, affecting odontoblast vitality.
Design: the aim of this study was to assess the differential transcriptome modulation induced by HEMA treatment in human cultured gingival fibroblasts (HGFs) at different exposure time compared to untreated cells.
Materials and methods: Gene expression profile was performed by employing a whole gene microarray approach on RNA extracted from cultured HGFs exposed to 3 mmol/l HEMA for 24 or 96 h. Differentially identified transcripts were analyzed by Ingenuity Pathways Analysis software to disclose genes biological functions.
Results: Hierarchical clustering analysis of the data set originated from a total of 8 experiments showed the selective presence of two gene clusters, composed by hundreds trandcripts differentially expressed after 24-h and 96-h HEMA treatment. when compared to untreated controls.
Functional analysis showed the transcripts involvement mainly in cell survival, proliferation and death, with an unbalance towards cell growth and inflammatory response.
Conclusions: Data analysis showed an overall damage induced by HEMA exposure for both HGFs cultures at 24 and 96-h mainly leading to a proliferation impairement. Interestingly 24-h HEMA exposure could induce the cells to trigger repair mechanisms evidencing an early compensatory response and survive while. 96-h incubation might increase apoptosis as a consequence of the chronic damage.

overall_design: Gene expression profile of Human Gingival Fibroblasts (HGFs) exposed to 3mM 2-Hydroxyethyl Methacrylate (HEMA) for 24- and 96-h versus untreated Human Gingival Fibroblasts at 24- and 96-h. A total of 8 experiments was carried out including biological and technical replicates.


title: Effects of Changes in Food Supply at the Time of Sex Differentiation on the Gonadal Transcriptome of Juvenile Fish. Implications for Natural and Farmed Populations

status: Public on Dec 25 2014

city: Barcelona

first: Noelia

last: Díaz Blanco

state: Barcelona

address: Passeig Marítim de la Barceloneta 37-49

department: Marine Renewable Resources

institute: Institute of Marine Sciences (ICM-CSIC)

summary:
Background: Food supply is a major factor influencing growth rates in animals. This has important implications for both natural and farmed fish populations, since food restriction may difficult reproduction. However, a study on the effects of food supply on the development of juvenile gonads has never been transcriptionally described in fish.
Methods and Findings: This study investigated the consequences of growth on gonadal transcriptome of European sea bass in: 1) 4-month-old sexually undifferentiated fish, comparing the gonads of fish with the highest vs. the lowest growth, to explore a possible link between transcriptome and future sex, and 2) testis from 11-month-old juveniles where growth had been manipulated through changes in food supply. The four groups used were: i) sustained fast growth, ii) sustained slow growth, iii) accelerated growth, iv) decelerated growth. The transcriptome of undifferentiated gonads was not drastically affected by initial natural differences in growth. Further, changes in the expression of genes associated with protein turnover were seen, favoring catabolism in slow-growing fish and anabolism in fast-growing fish. Moreover, while fast-growing fish took energy from glucose, as deduced from the pathways affected and the analysis of protein-protein interactions examined, in slow-growing fish lipid metabolism and gluconeogenesis was favored. Interestingly, the highest transcriptomic differences were found when forcing initially fast-growing fish to decelerate their growth, while accelerating growth of initially slow-growing fish resulted in full transcriptomic convergence with sustained fast-growing fish.
Conclusions: Food availability during sex differentiation shapes the juvenile testis transcriptome, as evidenced by adaptations to different energy balances. Remarkably, this occurs in absence of major histological changes in the testis.
Thus, fish are able to recover transcriptionally their testes if they are provided with enough food supply during sex differentiation; however, an initial fast growth does not represent any advantage in terms of transcriptional fitness if later food becomes scarce.

overall_design: Whole gonad transcriptome analysis from 35 individuals. Two sampling points at 133 days post fertilization (dpf) (7 individuals from the Fast growing group F and 8 from the Slow growing one S and at 332 dpf (5 individuals from each of the following groups: Fast growing-Fast growing FF; Fast growing-Slow growing FS; Slow growing-Fast growing SF and Slow growing-Slow growing SS).

last: Díaz

first: Laia

last: Ribas

first: Francesc

last: Piferrer