title: Comparative molecular assessment of implant adherent cells in smokers and non-smokers

status: Public on Nov 14 2015

city: Chapel Hill

first: Lyndon

last: Cooper

state: NC

address: 330 Brauer Hall, CB#7450

department: Prosthodontics

institute: UNC School of Dentistry

summary: Objective: to Identify the effect of surface texture on the modulation of gene transcription of implant adherent cells as influenced by the smoking habits of the subjects.

overall_design: Eighty four cp titanium implants with surface topographies exhibiting nanoscale features (Osseospeed-OS) and microrough surface without nanoscale features (TiOblast-TiO) were placed in the alveolar bone of 11 systemically healthy subjects and 10 smoking subjects and subsequently harvested at 3 and 7 days after placement. Total RNA was isolated from cells adherent to retrieved implants. A whole genome microarray using the Affymetrix Human gene 1.1 ST Array  was used to describe the gene expression profiles that were differentially regulated by the implant surfaces.

first: Ghadeer

last: Thalji

first: Salvador

last: Nares


title: Expression data to identify putative transcriptional targets of ZNF165 in Triple Negative Breast Cancer (TNBC)

status: Public on Nov 09 2015

city: Dallas

first: Angelique

last: Whitehurst

state: TX

address: 5323 Harry Hines Blvd.

department: Simmons Cancer Center

country: USA

institute: UT Southwestern

summary:
We found that the cancer testis antigen, ZNF165, is required for viability and can modulate TGFβ-induced gene expression in mesenchymal, Claudin-Low, TNBC. We employed the Affymetrix microarray platform to uncover transcriptionally modulated genes following ZNF165 depletion and TGFβ stimulation using the Claudin-low TNBC tumor-derived cell lines, SUM159 as a model. Our results provide insight into how ZNF165 globally modulates TGFβ signaling.
We used microarray analysis to uncover the transcriptional network controlled by ZNF165 and clarify the role of ZNF165 in global TGFβ signaling

overall_design: SUM159 and WHIM12 cells were reverse transfected with either non-targeting or ZNF165 siRNA. For SUM159 cells, sixty hours post-transfection, cells were exposed to TGFβ for 3 hours. For WHIM12, forty eight hours post-transfection, cells were exposed to TGFβ for 3 hours. Total RNA was isolated and hybridized on to Affymetrix microarrays. Each experiment was repeated three times.

middle: W

first: Kimberly

middle: E

last: Maxfield


title: Ni2+-dependent and PsaR-mediated regulation of the virulence genes pcpA, psaBCA, and prtA in Streptococcus pneumoniae

status: Public on Nov 20 2015

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Previous studies have shown that the transcriptional regulator PsaR regulates the expression of the PsaR regulon consisting of genes encoding choline binding protein (PcpA), the extracellular serine protease (PrtA), and the Mn2+-uptake system (PsaBCA), in the presence of manganese (Mn2+), zinc (Zn2+), and cobalt (Co2+). In this study, we explore the Ni2+-dependent regulation of the PsaR regulon. We have demonstrated by qRT-PCR analysis, metal accumulation assays, β-galactosidase assays, and electrophoretic mobility shift assays that an elevated concentration of Ni2+ leads to strong induction of the PsaR regulon. Our ICP-MS data show that the Ni2+-dependent expression of the PsaR regulon is directly linked to high, cell-associated, concentration of Ni2+, which reduces the cell-associated concentration of Mn2+. In vitro studies with the purified PsaR protein showed that Ni2+ diminishes the Mn2+-dependent interaction of PsaR to the promoter regions of its target genes, confirming an opposite effect of Mn2+ and Ni2+ in the regulation of the PsaR regulon. Additionally, the Ni2+-dependent role of PsaR in the regulation of the PsaR regulon was studied by transcriptome analysis.

overall_design:
Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type to D39 ΔpsaR grown in CDM with 0.3 mM Ni2+
One condition design comparision of two strains including a dye swap.

first: Irfan

last: Manzoor

first: Oscar

middle: P

last: Kuipers


title: A new metabolic route for the production of gamma-aminobutyric acid in Corynebacterium glutamicum

status: Public on Oct 22 2015

city: Bielefeld

first: João

middle: M. P.

last: Jorge

address: Universitätsstraße 25

country: Germany

institute: University of Bielefeld

summary: Corynebacterium glutamicum shows a great potential for the production of gamma-aminobutyric acid (GABA) from glucose fermentation via putrescine. GABA, a non-protein amino acid widespread in nature, is a component of pharmaceuticals, foods and the biodegradable plastic polyamide 4.  Here, the effect of GABA in the growth of C. glutamicum was evaluated. It was estimated that the presence 1.1 M of GABA in the medium reduces the maximum growth rate of C. glutamicum to half. It was also shown that the presence of GABA in the medium negatively affects the growth of C. glutamicum in ethanol as sole carbon source. Furthermore, a new route for the production of GABA in C. glutamicum was established. GABA production from glucose fermentation via putrescine was achieved by plasmid-based overexpression of putrescine transaminase (PatA) and gamma-aminobutyraldehyde dehydrogenase (PatD) in a putrescine production strain. The resultant strain can produce 5.3 ± 0.1 g L-1 of GABA. GABA production was improved by avoiding the formation of N-acetylputrescine and by reducing the amount of nitrogen in CGXII medium. Deletion of the genes responsible for GABA catabolism and GABA re-uptake led to an increase in the GABA production of 21% achieving a titer 8.0 ± 0.3 g L-1 and an increase in the volumetric productivity of 41% reaching a productivity of 0.31 g L-1 h-1, the highest volumetric productivity achieved so far for GABA production in C. glutamicum from glucose fermentation in flasks fermentations.  The results obtained hitherto are very promising and competitive compared to the traditional pathway for the production of GABA.

overall_design: Two conditions tested: 200 mM of NaCl vs 200 mM GABA supplemented in the culture medium. Control experiment done with the addition of 200 mM NaCl 2 technical replicates

middle: M

first: Volker

middle: F

last: Wendisch


title: Impact of galR delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Galactose

status: Public on Oct 30 2015

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔgalR  to D39 wild type grown in M17 medium+ 0.5% (w/v) galactose (GalM17).

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

first: Muhammad

last: Afzal


title: Impact of galR delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Glucose

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔgalR to D39 wild type grown in M17 medium+ 0.5% (w/v) glucose (GM17).


title: GalR Acts as a Transcriptional Activator of galKT in the Presence of Galactose in Streptococcus pneumoniae

summary:
We explored the regulatory mechanism of Leloir pathway genes in Streptococcus pneumoniae D39. Here, we demonstrate that the expression of galKT is galactose dependent. By microarray analysis and quantitative RT-PCR, we further show the role of the transcriptional regulator GalR, present upstream of galKT, as a transcriptional activator of galKT in the presence of galactose. Moreover, we predict a 19-bp regulatory site (5'-GATAGTTTAGTAAAATTTT-3' ) for the transcriptional regulator GalR in the promoter region of galK, which is also highly conserved in other streptococci. Growth comparison of Δ galK with the D39 wildtype strain grown in the presence of galactose shows that galK is required for the proper growth of S. pneumoniae on galactose.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Spinal Ependymoma Gene Expression Data

status: Public on Sep 02 2015

city: Houston

first: Stephen

middle: Mack

last: Christopher

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

summary:
Purpose: Myxopapillary ependymoma (MPE) is a distinct histological variant of ependymoma arising commonly in the spinal cord. Despite an overall favorable prognosis, distant metastases, subarachnoid dissemination, and late recurrences have been reported.  Currently the only effective treatment for MPE is gross-total resection. We characterized the genomic and transcriptional landscape of spinal ependymomas in an effort to delineate the genetic basis of this disease and identify new leads for therapy.

Experimental Design: Gene expression profiling was performed on 35 spinal ependymomas. Functional validation experiments were performed on tumour lysates consisting of assays measuring Pyruvate Kinase M activity (PKM), Hexokinase activity (HK), and lactate production.

Results: At a gene expression level, we demonstrate that spinal Grade II and MPE are molecularly and biologically distinct. These findings are supported by specific copy number alterations occurring in each histological variant. Pathway analysis revealed that MPE are characterized by increased cellular metabolism, associated with up-regulation of HIF-1α. These findings were validated by western blot analysis demonstrating increased protein expression of HIF-1α, HK2, PDK1, and phosphorylation of PDHE1A. Functional assays were performed on MPE lysates, which demonstrated decreased PKM activity, increased HK activity, and elevated lactate production.

Conclusions: Our findings suggest that MPE may be driven by a Warburg metabolic phenotype. The key enzymes promoting the Warburg phenotype: HK2, PKM2, and PDK are targetable by small molecule inhibitors/activators, and should be considered for evaluation in future clinical trials for MPE.

overall_design: RNA from 35 primary spinal ependymomas (fresh frozen) were isolated by pulverization in liquid nitrogen, and extraction using the Trizol Method (Invitrogen) [PMID:21840481]

middle: C

last: Mack

first: Michael

middle: D

last: Taylor


title: Expression data from monozygotic twins discordant for nicotine metabolism

status: Public on Sep 30 2015

city: Menlo Park

first: Aaron

last: Wacholder

state: CA

address: 333 Ravenswood Ave

department: Molecular Genetics Program

institute: SRI International

summary: The Nicotine Metabolic Ratio (NMR), the ratio of two stable metabolites of nicotine, cotinine and trans-3’hydroxycotinin, is a determinant of the number of cigarettes smoked per day (CPD), of smoking topography, responsiveness to treatment via transdermal nicotine for smoking cessation, and carcinogen activation and level. The predominant gene involved in nicotine metabolism is CYP2A6, a highly polymorphic locus located in a cluster of P450 cytochrome protein loci on chr19q13. A recent study comprehensively modeling CYP2A6 genetic variation at seven polymorphisms and a related Nicotine Metabolic Ratio, the cotinine: cotinine+nicotine ratio, explains 72% of NMRC/C+N variation. These results suggest that additional genes may be contributing to nicotine and cotinine metabolism directly or via interaction with CYP2A6 or other genes.  To identify additional genes that may influence the NMR, we conducted a genome-wide gene expression analysis of lymphoblastoid cell line (LCL) gene expression in a sample of monozygotic twins discordant for the NMR.

overall_design: Eight individuals (four monozygotic twin pairs), each with three replicates for a total of 24 samples

first: Andrew

last: Bergen

first: Denise

last: Nishita

first: Martha

last: Michel

first: Ruth

last: Krasnow

first: Harold

middle: S

last: Javitz

first: Douglas

middle: A

last: Fugman

first: Jay

last: Tischfield

first: Hy

last: Hops

first: Neal

middle: L

last: Benowitz

first: Mary-Anne

last: Enoch

first: Gary

last: Swan


title: Transcriptome analysis during seed development provides insights into altered gene expression in Glycine max

status: Public on Aug 11 2015

city: New Delhi

first: Archana

last: Sachdev

state: NCR Delhi

address: Pusa campus

department: Biochemistry

country: India

institute: Indian Agricultural Research Institute

summary:
The temporal expression profile of Glycine max seeds was carried out to identify genes that are differentially expressed (DE) during seed development. Using the Affymetrix chip, we have for the first time provided a holistic view of the transcriptional landscape during seed development in four different developmental stages in Glycine max. cv. Pusa 16. The analysis of the differential expression patterns and functional category enrichment of DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have led to the identification of few candidate genes related to inositol metabolism and especially in phytate biosynthesis.
In conclusion, we have shown here a logical approach to identify possible candidate genes for fine tuning the metabolic flux for phytate generation, which may be altered by metabolic engineering in developing a low phytate phenotype.

overall_design: Seeds of Glycine max grown at 28/26°C, 16h/8h light/dark were collected at different developmental stages( 0-4mm, 4-8mm, 8-12mm and 12-16mm ) and analyzed. Samples in triplicates from each developmental stage were used for data generation on Affymetrix Chip, each time the earlier developmental stage was considered as  control Vs the treatment, corresponding to the later developmental stage. For each biological replicates, RNA was extracted from 20 seeds collected from 5 different plants, grown in the same conditions using the Trizol method. RNA integrity was analyzed using bio analyzer (with RIN value more than 8).

first: A

first: M

last: Punjabi

first: V

last: Krishnan

last: Jolly

last: Hada

first: N

last: Basak

last: Pandey

last: Marathe

first: R

last: Kansal

last: Dahuja

first: C

last: Viswanathan

last: Rai


title: Cold acclimation improves insulin sensitivity in patients with type 2 diabetes mellitus.

status: Public on Jul 05 2015

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Background: The prevalence of type 2 diabetes has increased dramatically in recent decades. Increasing brown adipose tissue (BAT) mass and activity has recently emerged as an interesting approach to not only increase energy expenditure, but also improve glucose homeostasis. BAT can be recruited by prolonged cold exposure in lean, healthy humans. Here, we tested whether cold acclimation could have therapeutic value for patients with type 2 diabetes by improving insulin sensitivity. Methods: Eight type 2 diabetic patients (age 59.3±5.8 years, BMI 29.8±3.2 kg/m2) followed a cold acclimation protocol, consisting of intermittent cold exposure (6 hours/day, 14-14.5 °C) for 12 consecutive days. Before and after cold acclimation, cold-induced BAT activity was assessed by  [18F]FDG-PET/CT scanning, insulin sensitivity at thermoneutrality by a hyperinsulinemic-euglycemic clamp, and muscle and WAT biopsies were taken. Results: Cold-induced BAT activity was low, but increased in all patients upon cold acclimation (SUV from 0.40±0.29 to 0.63±0.78, p<0.05). Interestingly, insulin sensitivity showed a very pronounced 40% increase upon cold acclimation (glucose rate of disappearance from 14.9±4.1 to 20.5±6.9 μmol kg-1 min-1, p<0.05). A 40% increase in insulin sensitivity cannot be explained by BAT glucose uptake, in fact basal skeletal muscle GLUT4 content and translocation was markedly increased after cold acclimation, without effects on insulin signaling or AMPk activation. Conclusions: Regular mild cold exposure has marked effects on insulin sensitivity, which are accompanied by small increases in BAT activity and more pronounced effects on skeletal muscle. These data suggest a novel therapeutic option for the treatment of type 2 diabetes.

overall_design: Microarray analysis was performed on abdominal subcutaneous white adipose tissue samples from human type 2 diabetic patients before, and after 10 days of cold acclimation. A total of 14 samples, from 7 subjects, were used for the microarray analysis.

first: Mark

middle: J

last: Hanssen

first: Joris

last: Hoeks

middle: V

last: Boekschoten

first: Sander

last: Kersten

first: Wouter

last: Marken Lichtenbelt

first: Patrick

last: Schrauwen


title: The effect of statins on blood gene expression in COPD

status: Public on Jul 23 2015

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

country: Canada

institute: PROOF Centre of Excellence

summary: Background: COPD is currently the fourth leading cause of death worldwide and predicted to rank third by 2020. Statins are commonly used lipid lowering agents with documented benefits on cardiovascular morbidity and mortality, and have also been shown to have pleiotropic effects including anti-inflammatory and anti-oxidant activity.   Objective: Identify a gene signature associated with statin use in the blood of COPD patients, and identify molecular mechanisms and pathways underpinning this signature that could explain any potential benefits in COPD.  Methods: Whole blood gene expression was measured on 168 statin users and 452 non-users from the ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) study. Gene expression was measured using the Affymetrix  Human Gene 1.1 ST microarray chips. Factor Analysis for Robust Microarray Summarization (FARMS) was used to process the expression data and to filter out non-informative probe sets. Differential gene expression analysis was undertaken using the Linear Models for Microarray data (Limma) package adjusting for propensity score and employing a surrogate variable analysis. Similarity of the expression signal with published gene expression profiles was performed in ProfileChaser.  Results: 18 genes were differentially expressed between statin users and non-users at a false discovery rate of 10%. Top genes included LDLR, ABCA1, ABCG1, MYLIP, SC4MOL, and DHCR24.  The 18 genes were significantly enriched in pathways and biological processes related to cholesterol homeostasis and metabolism, and were enriched for transcription factor binding sites for sterol regulatory element binding protein 2 (SREBP-2). The resulting gene signature showed correlation with Huntington disease, Parkinson’s disease and acute myeloid leukemia.   Conclusion: Statins gene signature was not enriched in any pathways related to respiratory diseases, beyond the drug’s effect on cholesterol homeostasis.

overall_design: Study subjects were a subset of those with COPD from the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE) study (Vestbo et al.), funded by GlaxoSmithKline (GSK Study No. SCO104960, NCT00292552). ECLIPSE is a non-interventional, observational, multicentre, three-year study in people with COPD.  Blood was collected in PAXGene tubes and frozen at -80oC.  In this work we have looked at the effect of statins on gene expression in 620 subjects of whom 168 were statin users.  ECLIPSE study was described in: Vestbo J, Anderson W, Coxson HO, et al.: Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-points (ECLIPSE). Eur Respir J. 2008;31(4):869-73


title: Difference in gene expression between WT (Col-0) and atxrn4-3 mutant under non-stress and heat stress condition

status: Public on Jul 14 2015

city: Yokohama

first: Motoaki

last: Seki

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

country: Japan

institute: RIKEN CSRS

summary: Arabidopsis 5’-3’ exoribonuclease, AtXRN4, a homolog of yeast Xrn1p, functions in degradation of uncapped RNAs after de-capping step. While Xrn1p-dependent on plant XRN4’s targets for degradation is still limited. For understanding biological function of AtXRN4, we tested survivability of atxrn4 mutants under heat stress. Our results showed that atxrn4 mutants increased survival rate under short-term degradation is a main mRNA decay in yeast, knowledge heat stress compared with WT plants. Our microarray and mRNA decay assay showed that loss of AtXRN4 function caused reduction of mRNA degradation of heat shock factor A2 (HSFA2) and ethylene response factor 1 (ERF1). HSFA2 has been known as a key regulator in heat acclimation, was found as a target for AtXRN4 for degradation at non-stress condition. Heat stress applied on atxrn4-3 hsfa2 double mutant severely lacked heat tolerance phenotype of atxrn4 mutant. These results suggest that AtXRN4-mediated mRNA degradation linked to suppress heat acclimation.

overall_design: In the study here, 2 week-old WT and atxrn4-3 mutant plants were exposure to non-stress (22oC) and heat-stress (37oC, 1 h). Custom microarray was applied to acquire expression profile of 32788 Arabidopsis genes. 3 biological repeats of WT (non-stress), WT(heat stress), atxrn4-3 (non-stress) and atxrn4-3 (heat stress) were used for microarray analysis

first: Anh Hai

last: Nguyen

first: Akihiro

last: Matsui

first: Maho

last: Tanaka

first: Kei

last: Iida


title: microRNA expression levels as predictors of outcome in pediateric acute lymphoblastic leukemia (ALL) patients

status: Public on Jun 01 2015

city: Petach Tikva

first: Smadar

last: Avigad

address: 14 Kaplan Street

department: Pediatric Hematology Oncology

country: Israel

institute: Schneider Children's Medical Center of Israel

summary: Expression levels of specific microRNAs were significantly associated with adverse clinical parameters of pediatric ALL patients and might serve as novel biomarkers for outcome, at diagnosis, in these patients.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: microRNA-array analysis was performed on BM samples, at diagnosis, of 48 pediatric ALL patients. The expression levels were correlated to established clinical prognostic markers such as age, cell of origin (T-cell or B-cell), white blood count, prednisone response and relapse.

first: Iedan

middle: R

last: Verly


title: Identification of differentially expressed genes between developing seeds of different soybean cultivars

status: Public on Apr 29 2015

city: St Paul

first: Susan

middle: I

last: Gibson

state: MN

address: 1500 Gortner Ave

department: Plant Biology

institute: University of Minnesota

summary: Soybean is a rich source of protein and oil and a primary feedstock for biodiesel production.  Previous research on soybean indicated that protein, oil and yield are controlled quantitatively in soybean seeds. However, genetic mechanisms controlling seed composition and yield in soybean remain unknown. We used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean varieties, which differ in seed weight, yield, protein content and oil content. Some of the differentially expressed genes identified in this study may play important roles in controlling these traits.

overall_design: The soybean plants of two soybean varieties Minsoy and Archer and two recombinant inbred lines from the cross that are similar in maturity but differ in yield were grown in St Paul, Minnesota during the summers of 2007 and 2008.  In 2007, each line was planted as a single row. In 2008, a randomized complete block (RCB) design was used and each line had 3 replicates planted 1-2 weeks apart. Within each replicate, two rows per line were planted. Seeds were harvested at three developmental stages, namely, seed length = 2 mm, 3.5 mm, and 5-6 mm, which correspond approximately to soybean reproductive stages R4, R5 and early R6, respectively.  In 2007 three independent samples were collected for each line and developmental stage.  In 2008, two seed samples (one from each row) were collected for each line at each stage within each replicate.  The pairs of seed samples were then pooled.  Thus, three sets of independent tissue samples were collected for RNA extraction and hybridization on Affymetrix microarrys.

first: Rongshuang

last: Lin

first: Jane

last: Glazebrook

first: Fumiaki

last: Katagiri

first: James

middle: H

last: Orf


title: The transcirptional effect of CtrA depletion in S. meliloti

status: Public on Apr 24 2015

first: Nicole

middle: Janell

last: De Nisco

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UTSW Medical Center

summary:
We wanted to test the effect on global gene expression of depleting the essential cell cycle regulator CtrA in order to determine the genes both indirectly and directly transcriptionally regulated by CtrA
Gene expression changes in S. meliloti 1,2,4 and 6 hours post CtrA depletion

overall_design: Log-phase S. meliloti cultures carrying an IPTG-inducible allele of CtrA were split and transferred to growth media lacking IPTG (depletion) and with 1mM IPTG (control). Samples for RNA extraction were taken 1,2,4, and 6 hours after the start of the depletion experiment to monitor gene expression changes in the population after different periods of CtrA depletion.

first: Graham

last: Walker


title: High fat challenges with different fatty acids affect distinct atherogenic gene expression pathways in immune cells from lean and obese subjects

status: Public on May 13 2015

first: Guido

last: Hooiveld

summary:
Early perturbations in vascular health can be detected by imposing subjects to a high fat (HF) challenge and measure response capacity. Subtle responses can be determined by assessment of whole-genome transcriptional changes. We aimed to magnify differences in health by comparing gene-expression changes in peripheral blood mononuclear cells (PBMCs) towards a high MUFA or SFA challenge between subjects with different cardiovascular disease risk profiles and to identify fatty-acid specific gene-expression pathways.
METHODS AND RESULTS: In a cross-over study, 17 lean and 15 obese men (50-70y) received two 95g fat shakes, high in SFAs or MUFAs. PBMC gene-expression profiles were assessed fasted and 4h postprandially. Comparisons were made between groups and shakes. During fasting, 294 genes were significantly different expressed between lean and obese. The challenge increased differences to 607 genes after SFA and 2516 genes after MUFA. In both groups, SFA decreased expression of cholesterol biosynthesis and uptake genes and increased cholesterol efflux genes. MUFA increased inflammatory genes and PPARα targets involved in β-oxidation.
CONCLUSION: Based upon gene-expression changes, we conclude that a HF challenge magnifies differences in health, especially after MUFA. Our findings also demonstrate how SFAs and MUFAs exert distinct effects on lipid handling pathways in immune cells.

overall_design: In a double-blind cross-over study, 17 lean and 15 obese men (aged 50-70y) received two high-fat milkshakes containing 95g fat, either high in saturated (SFA) or monounsaturated (MUFA) fatty acids. PBMC gene expression profiles were determined before and 4h after shake consumption.

first: Diederik

last: Esser

first: Lydia

last: Afman


title: Impact of malR delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Glucose

status: Public on Apr 23 2015

first: Sulman

last: Shafeeq

summary: Transcriptome Comparison of the Streptococcus pneumoniae D39 ΔmalR mutant to D39 wild type grown in GM17 (0.5 % (w/v) Glucose + M17) medium.

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

first: Muhammad

last: Afzal

first: Irfan

last: Manzoor

first: Oscar

middle: P

last: Kuipers


title: Gene expression changes in U937 cells in response to ectopic expression of EVI1 and/or etoposide treatment

status: Public on Mar 10 2015

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

summary:
Overexpression of ecotropic viral integration site 1 (EVI1) is associated with aggressive disease in acute myeloid leukemia (AML). Despite of its clinical importance, little is known about the mechanism through which EVI1 confers resistance to antileukemic drugs. Here, we show that a human myeloid cell line constitutively overexpressing EVI1 after infection with a retroviral vector (U937_EVI1) was partially resistant to etoposide and daunorubicin as compared to empty vector infected control cells (U937_vec). Similarly, inducible expression of EVI1 in HL-60 cells decreased their sensitivity to daunorubicin. Gene expression microarray analyses of U937_EVI1 and U937_vec cells cultured in the absence or presence of etoposide showed that 77 and 419 genes were regulated by EVI1 and etoposide, respectively. Notably, mRNA levels of 26 of these genes were altered by both stimuli, indicating that EVI1 regulated genes were strongly enriched among etoposide regulated genes and vice versa. One of the genes that were induced by both EVI1 and etoposide was CDKN1A/p21/WAF, which in addition to its function as a cell cycle regulator plays an important role in conferring chemotherapy resistance in various tumor types. Indeed, overexpression of CDKN1A in U937 cells mimicked the phenotype of EVI1 overexpression, similarly conferring partial resistance to antileukemic drugs.
Rommer A, Steinmetz B, Herbst F, Hackl H, Heffeter P, Heilos D, Filipits M, Steinleitner K, Hemmati S, Herbacek I, Schwarzinger I, Hartl K, Rondou P, Glimm H, Karakaya K, Krämer A, Berger W, and Wieser R: EVI1 Inhibits Apoptosis Induced by Antileukemic Drugs via Upregulation of CDKN1A/p21/WAF in Human Myeloid Cells. PLoS One 8(2):e56308 (2013). doi: 10.1371/journal.pone.0056308.

overall_design: U937 cells transduced with an EVI1 expression vector or empty vector as control were treated or not with 400 nM etoposide for 48h. 2 biological replicate experiments were performed.

first: Anna

last: Rommer

first: Hubert

last: Hackl


title: Highly efficient in vivo delivery of functional RNAs using new versatile MS2-chimeric retrovirus-like particles

status: Public on Mar 11 2015

city: Toulouse

first: Anne

last: PREL

address: 1 Avenue J Poulhes

department: Stromalab

country: France

institute: CNRS 5273 INSERM1031

summary:
RNA delivery is a method of choice to achieve transient gene expression for research and in cell- or gene-based therapies. To improve retroviral transfer, we designed a dimerization-independent MS2-driven packaging system using MS2-retrovirus chimeras. We delivered RUNX2- or DLX5-mRNA into primary human bone-marrow mesenchymal-stem-cells.
We used microarrays to detail the global programme of gene expression confirming the effects of pro-osteogenic genes transduced by MS2 chimeric lentiviral particles.

overall_design:
Immature bone marrow mesenchymal stem cells were transduced with viral particles containing either MS2RLP-DLX5 or MS2RLP-RUNX2 or IDLV-Luc as control. Thirty hours after the first transduction, cells were transduced again as above. At 58 h, cells were washed 3 times with PBS and harvested. mRNA were then extracted.

Please note that data analyses were done in 3 groups;
GSM1630700-GSM1630707
GSM1630708-GSM1630715
GSM1630716-GSM1630723

last: Prel

first: Frédéric

last: Deschaseaux

first: Jean-Christophe

last: Pagès


title: Fucose-mediated transcriptional activation of the fcs operon by FcsR in Streptococcus pneumoniae

summary: In this study, we explore the impact of fucose on the transcriptome of S. pneumoniae D39. The expression of various genes and operons, including the fucose uptake PTS and utilization operon (fcs operon), was altered in the presence of fucose. By means of quantitative RT-PCR and β-galactosidase analysis, we demonstrate the role of the transcriptional regulator FcsR, present upstream of the fcs operon, as a transcriptional activator of the fcs operon. We also predict a 19-bp putative FcsR regulatory site (5’-ATTTGAACATTATTCAAGT-3’) in the promoter region of the fcs operon. The functionality of this predicted FcsR regulatory site was further confirmed by promoter-truncation experiments, where deletion of half of the FscR regulatory site or full deletion led to the abolition of expression of the fcs operon.

overall_design:
Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in M17 plus 0.5% glucose (GM17) to grown in M17 plus 0.5% fucose (FM17).
Two conditions design comparison of one strain including a dye swap.


title: A gene expression profile associated with relapse of cytogenetically normal acute myeloid leukemia is enriched for leukemia stem cell genes

status: Public on Mar 16 2015

summary: Relapse, associated with therapy resistance, is a major clinical problem in acute myeloid leukemia (AML), yet little is known about the underlying molecular mechanisms. Using genome wide gene expression profiling on 11 paired samples from diagnosis and relapse, we show that the expression of a substantial number of genes was altered in a highly consistent manner between these disease stages. Furthermore, the relapse associated gene expression profile was significantly enriched for leukemia stem cell (LSC) genes, indicating that recurring AML is characterized by increased stemness, and supporting the concept that it is due to the outgrowth of chemotherapy resistant LSCs.

overall_design: Paired peripheral blood samples from the times of diagnosis and relapse were obtained from 11 patients with cytogenetically normal AML. cRNA was hybridized to Affymetrix human ST1.1 arrays.


title: Maltose-dependent transcriptional regulation of the mal regulon by MalR in Streptococcus pneumoniae

summary:
The maltose regulon (mal regulon) has previously been shown to consist of the mal gene cluster (malQP, malXCD and malAR operons) in Streptococcus pneumoniae. In this study, we have further elucidated the complete mal regulon in S. pneumoniae D39 using microarray analyses and β-galactosidase assays. In addition to the mal gene cluster, the complete mal regulon of S. pneumoniae D39 consists of a pullulanase (PulA), a glucosidase (DexB), a glucokinase (RokB), a PTS component (PtsG) and an amylase (AmyA2). Our microarray studies and β-galactosidase assays further showed that the LacI-family transcriptional regulator MalR represses the expression of the mal regulon in the absence of maltose. Furthermore, the role of the pleiotropic transcriptional regulator CcpA in the regulation of the mal regulon in the presence of maltose was also explored. Our microarray analysis with a ΔccpA strain showed that CcpA only represses the expression of the malXCD operon and the pulA gene in the presence of maltose.

This SuperSeries is composed of the SubSeries listed below.


title: Zebrafish early transcriptional response to viral haemorrhagic septicemia rhabdovirus (VHSV) challenge vs2

status: Public on Apr 17 2015

city: Madrid

first: Julio

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

summary: We describe here  the  transcripts induced after infection of zebrafish with viral haemorrhagic septicemia rhabdovirus (VHSV). Two days after infection, differentially expressed transcript levels from selected immune-related zebrafish genes were studied in both fins and internal organs (pooled spleen, head kidney and liver).

overall_design: VHSV-induced gene expression in zebrafish fins and organs was measured at 2 days after infection. Four independent experiments were performed for each treatment and their corresponding controls

first: Paloma

last: Encinas


title: Transcriptional response of Streptococcus pneumoniae D39 to sialic acid

status: Public on Mar 06 2015

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in M17 medium toD39 wild-type grown in M17 medium + 0.5% sialic acid (SM17).

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

first: Hifza

last: Ahmed


title: Impact of ccpA delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of sialic acid

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔccpA to D39 wild-type grown in M17 medium + 0.5% sialic acid (SM17).

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


title: Zebrafish immune response to bacterial and viral infection

status: Public on May 12 2015

summary: In order to explore the relative importance of adult zebrafish innate and adaptive immune responses to different kinds of infections, we compared the gene expression profile of VHSV-challenge-survivors, bacterial infection survivors  and control non infected zebrafish.

overall_design:
VHSV -infection-survivors zebrafish were divided in two groups of 12 individuals, first group was infected with VHSV (samples named A) and second group was mock-infected (samples named B). Two days after challenge, zebrafish of each group were divided in four subgroups (3 fishes per group) and head kidney and spleen  of each individual were sampled. For each group, internal organs of three fishes were pooled, so four biological replicates were generated .
Zebrafish surviving a natural infection caused by Aeromonas hydrophila and  Vibrio fluvialis (samples named C) were divided in four groups (3 fishes per group) and head kidney and spleen were extracted. Finally, 12 healthy zebrafish were used as control group (samples named D) and processed in the same way as group C.


title: Impact of ccpA delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Maltose

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔccpA  to D39 wild-type grown in MM17 (0.5 % (w/v) Maltose + M17) medium


title: Impact of ccpA delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Glucose

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔccpA to D39 wild-type grown in M17 medium + 0.5% glucose (GM17).


title: Transcriptional response of Streptococcus pneumoniae D39 to Maltose

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in MM17 (0.5 % (w/v) Maltose + M17) to grown in GM17 (0.5 % (w/v) Glucose + M17).


title: Sialic acid-mediated gene expression in Streptococcus pneumoniae and the role of NanR as a transcriptional activator of the nan gene cluster

summary:
In this study, we investigated the transcriptomic response of Streptococcus pneumoniae D39 to sialic acid (N-acetylneuraminic acid: Neu5Ac). Transcriptome comparison of the D39 wild-type grown in M17 medium with and without sialic acid revealed the elevated expression of various genes and operons including the nan gene cluster (nan operon-I and nanA gene). Our microarray analysis and promoter-lacZ fusion studies showed that the transcriptional regulator NanR acts as a transcriptional activator of nan operon-I and the nanA gene in the presence of sialic acid. The putative regulatory site of NanR in the promoter region of nan operon-I is predicted and confirmed by promoter truncation experiments. Furthermore, the role of CcpA in the regulation of the nan gene cluster is demonstrated through microarray analysis and promoter-lacZ fusion studies, suggesting that in the presence of sialic acid and glucose, CcpA represses the expression of nan operon-I while the expression of the nanA gene is CcpA-independent.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Impact of nanR delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of sialic acid

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔnanR to D39 wild-type grown in M17 medium + 0.5% sialic acid (SM17).


title: Transcriptomic profiles of skin fibroblasts from patients affected by schizophrenia and controls

status: Public on Feb 17 2015

city: Brescia

first: Nadia

last: Cattane

state: BS

address: Viale Europa 11

department: Department of Translational and Molecular Medicine

country: Italy

institute: University of Brescia

summary:
Whole-genome expression studies in peripheral tissues of patients affected by schizophrenia (SCZ) can provide new insights into the molecular basis of the disorder and  innovative biomarkers that may be of great usefulness in the clinical practice. Recent evidence suggests that skin fibroblasts could represent a non-neural peripheral model useful to investigate molecular alterations in psychiatric disorders.
A microarray expression study was conducted comparing transcriptomic profiles of skin fibroblasts from SCZ patients and controls. Fibroblasts can be more advantageous to discover mental disorder aetiological mechanisms since they seem more similar to neurons and less affected by the environmental confounders.

overall_design: Transcriptomic profiles of human skin fibroblasts obtained from 20 schizophrenia patients were compared to 20 controls

first: Alessandra

last: Minelli

first: Elena

last: Milanesi

first: Carlo

last: Maj

first: Stefano

last: Bignotti

first: Marco

last: Bortolomasi

first: Luisella

last: Bocchio-Chiavetto

first: Massimo

last: Gennarelli


title: Impact of ulaR2 delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of ascorbic acid

status: Public on Jan 21 2015

first: Sulman

last: Shafeeq

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔulaR2 to D39 wild-type grown in M17 medium + 10mM ascorbic acid (AM17.

first: Muhammad

last: Afzal

first: Oscar

last: Kuipers


title: Transcriptional response of Streptococcus pneumoniae D39 to ascorbic acid

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in M17 medium to grown in M17 medium + 10mM ascorbic acid (AM17).

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


title: A healthy Nordic diet has a beneficial influence on the expression of genes involved in inflammation in subcutaneous adipose tissue

status: Public on Jan 26 2015

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

institute: Karolinska

summary:
In a randomized controlled dietary intervention study we compared an isocaloric Healthy Nordic diet with the average Nordic diet for influence on abdominal subcutaneous adipose tisse gene expression. We studied obese adults with features of the metabolic syndrom, n=56. There was no significant difference in age, BMI, or gene expression between the groups before the intervention. The intervention lasted for 18-24 weeks.
Gene expression was analyzed using linear mixed-effects models including specific genes as dependent variable, subject identifier as a random effect, and body weight, age, gender, study centre (i.e. also study duration), study group, time-point and study group * time-point interaction as covariates. 128 genes were significantly different regulated by the two diets with a FDR of 24%. TThese genes were overrepresented in pathways related to immune response. I conclusion, a Healthy Nordic diet reduces inflammatory gene expression in abdominal subcutaneous adipose tissue. This could contribute to beneficial influences on lipid metabolism and cardiovascular disease.

overall_design: Abdominal subcutaneous adipose needle biopsies were obtained before (W0) and after completion (W18-24) of the dietary intervention. From the biopsies we extracted RNA. From total RNA we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.1 ST Arrays (Affymetrix Inc., Santa Clara, CA), and then washed, stained and scanned the slides using standardised protocols (Affymetrix Inc.).


title: ASA404 and TNFα treatment in preclinical models of endocrine tumors is associated with differential TNF-R 1 and TLR- 4 –signaling

status: Public on Dec 17 2014

city: München

first: Carsten

last: Jäckel

address: Schillerstr 42

department: Klinische Biochemie

institute: Klinikum der Universität München, Klinische Biochemie

summary: Purpose: ASA404 (Vadimezan) belongs to a class of agents with disrupting properties against tumor vasculature, which is partly mediated by TNFα-signaling. Our aim was to investigate the potential therapeutic applicability of ASA404 against endocrine tumors.  Experimental Design: We determined anti-tumoral effects in preclinical models of neuroendocrine tumors of the gastroenteropancreatic system [1] and adrenocortical cancer (NCI-H295R) by histology and immunohistochemistry. Furthermore, we characterized these models with their clearly different responsiveness regarding TNFα synthesis and signaling.   Results: Upon treatment of tumor bearing mice significant anti-tumoral effects, an increase in TNFα as well as TNFα-specific activation of downstream signaling were evident in the BON tumor model while no comparable effects were detectable for NCI-H295R. Two important modulator of TNFα-signaling, toll-like-receptor 4 (TLR-4) and its adaptor protein LY96 were found highly expressed in BON tumors and transgenic expression in NCI-H295R partly restored TNFα responsiveness. Furthermore, expression of IRAK2-kinase, which has recently been linked to TLR-4-signaling as a mediator of sustained TNFα release was induced upon TNFα-treatment in BON, but not in NCI-H295R cells. Finally, we identified TNFAIP3/A20, a member of an inhibitory feedback-loop downstream of both investigated signaling cascades, as overexpressed in the adrenocortical carcinoma tumor model. Subsequent analyses of clinical patient samples confirmed a correlation between tumor TNFAIP3 expression levels and overall survival in patients with ACC.  Conclusions: Taken together our findings provide evidence that modulation of TNFα-signaling could be of relevance both for the clinical course of ACC patients and as a marker of treatment response.

overall_design: BON or NCI-H295R tumor cells were treated in-vitro with TNFalpha and compared to unstimulated cells

first: Constanze

last: Hantel

first: Alexandra

last: Ozimek

first: Regia

last: Lira

first: Bruno

last: Ragazzon

first: Roman

last: Frantsev

first: Martin

last: Reincke

first: Jérôme

last: Bertherat

first: Thomas

last: Mussack

first: Felix

last: Beuschlein


title: Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation [Affymetrix]

status: Public on Jan 20 2015

city: La Jolla

first: Daniel

last: Salomon

address: 10550 N Torrey Pines Rd, MEM-241

department: Molecular & Experimental Medicine

institute: The Scripps Research Institute

summary: Memory T cells are primed for rapid responses to antigen; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpG) mapped by deep sequencing to T cell activation in human naïve and memory CD4 T cells. 466 CpGs (132 genes) displayed differential methylation between naïve and memory cells. 21 genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 genes encode proteins closely studied in T cells while 15 genes represent novel targets for further study. 39 genes exhibited reduced methylation in memory cells coupled with increased gene expression with activation compared to naïve cells, revealing specific genes more rapidly expressed in memory compared to naïve cells and potentially regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells and correlated with activation-induced gene expression.

overall_design: transcriptome of primary human naïve and memory CD4 T cells at rest and 48 hours post-activation.

first: H

middle: K

last: Komori

first: G

middle: T

last: Hart

first: Sarah

last: LaMere

first: Pamela

last: Chew


title: Analyzing cold tolerance mechanism in transgenic zebrafish (Danio rerio)

status: Public on Dec 23 2014

city: Qingdao

first: Qian

last: Wang

address: 7 Nanhai Road

country: China

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: Low temperatures may cause severe growth inhibition and mortality in fish. In order to understand the mechanism of cold tolerance, a transgenic zebrafish Tg (smyd1:m3ck) model was established to study the effect of energy homeostasis during cold stress. The muscle-specific promoter Smyd1 was used to express the carp muscle form III of creatine kinase (M3-CK), which maintained enzymatic activity at a relatively low temperature, in zebrafish skeletal muscle. In situ hybridization showed that M3-CK was expressed strongly in the skeletal muscle. When exposed to 13°C, Tg (smyd1:m3ck) fish maintained their swimming behavior, while the wild-type could not. Energy measurements showed that the concentration of ATP increased in Tg (smyd1:m3ck) versus wild-type fish at 28°C. After 2 h at 13°C, ATP concentrations were 2.16-fold higher in Tg (smyd1:m3ck) than in wild-type (P < 0.05). At 13°C, the ATP concentration in Tg (smyd1:m3ck) fish and wild-type fish was 63.3% and 20.0%, respectively, of that in wild-type fish at 28°C. Microarray analysis revealed differential expression of 1249 transcripts in Tg (smyd1:m3ck) versus wild-type fish under cold stress. Biological processes that were significantly overrepresented in this group included circadian rhythm, energy metabolism, lipid transport, and metabolism. These results are clues to understanding the mechanisms underlying temperature acclimation in fish.

overall_design: Gene expression in triplicate samples of m3ck-13°C, m3ck-28°C, wt-13°C, and wt-28°C was assessed. Twelve microarray experiments were performed, each with three fish.

first: Xungang

last: Tan

first: Shuang

last: Jiao

first: Feng

last: You

first: Pei-Jun

last: Zhang


title: Gene expression profile of sporadic and PSEN1 early-onset Alzheimer’s Disease

city: Barcelona

first: Anna

last: Antonell

address: C/Casanova, 143

department: Unitat d'Alzheimer i altres transtorns cognitius

institute: Hospital Clínic Barcelona

summary: Alzheimer’s disease (AD) is the most common neurodegenerative dementia. Around 10% of cases present an age of onset before 65 years-old, which in turn can be divided in monogenic or familial AD (FAD) and sporadic early-onset AD (EOAD). Mutations in PSEN1, PSEN2 and APP genes have been linked with FAD. The aim of our study was to describe the brain whole-genome RNA expression profile of the posterior cingulate area in EOAD and FAD caused by PSEN1 mutations (FAD-PSEN1). 14 patients (7 EOAD and 7 FAD-PSEN1) and 7 neurologically healthy controls were selected and samples were hybridized in a Human Gene 1.1 microarray from Affymetrix. When comparing controls with EOAD and controls with FAD-PSEN1, we found 3183 and 3351 differentially expressed genes (DEG) respectively (FDR corrected p<0.05). However, any DEG was found in the comparison of the two groups of patients. Microarrays were validated through quantitative-PCR of 17 DEG. In silico analysis of the DEG revealed an alteration in biological pathways related to calcium-signaling, axon guidance and long-term potentiation (LTP), among others, in both groups of patients. These pathways are mainly related with cell signalling cascades, synaptic plasticity and learning and memory processes. In conclusion, the altered biological final pathways in EOAD and FAD-PSEN1 are highly coincident. Also, the findings are in line with those previously reported for late-onset AD (LOAD, onset >65 years-old), which implies that the consequences of the disease at the molecular level are similar in the final stages of the disease.

overall_design: 21 Samples were analyzed: 7 controls, 7 Early-onset Alzheimer's disease (AD) patients and 7 early-onset AD genetically determined by a mutation in PSEN1 gene.

first: Albert

last: Lladó

first: Jordi

last: Altirriba

first: Teresa

last: Botta-Orfila

first: Mircea

last: Balasa

first: Manel

last: Fernández

first: Isidre

last: Ferrer

first: Raquel

last: Sánchez-Valle

first: José

last: Molinuevo


title: Ascorbic acid-dependent gene expression in Streptococcus pneumoniae and the activator function of the transcriptional regulator UlaR2.

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

institute: Karolinska Institutet

summary:
In this study, we have explored the impact of ascorbic acid on the transcriptome of Streptococcus pneumoniae D39. The expression of several genes and operons, including the ula operon (which has been previously shown to be involved in ascorbic acid utilization), the AdcR regulon (which has been previously shown to be involved in zinc transport and virulence) and a PTS operon (which we denote here as ula2 operon) were altered in the presence of ascorbic acid. The ula2 operon consists of five genes, including the transcriptional activator ulaR2. Our β-galactosidase assay data and transcriptome comparison of the ulaR2 mutant with the wild-type demonstrated that the transcriptional activator UlaR2 in the presence of ascorbic acid activates the expression of the ula2 operon. We further predict a 16-bp regulatory site (5’-ATATTGTGCTCAAATA-3’) for UlaR2 binding in the Pula2. Furthermore, we have explored the effect of ascorbic acid on the expression of the AdcR regulon. Our ICP-MS analysis showed that addition of ascorbic acid to the medium causes zinc starvation in the cell that leads to the activation of the AdcR regulon.

This SuperSeries is composed of the SubSeries listed below.


title: miRNA-transcriptome expression pattern during differentiation in human skeletal muscle cells

status: Public on Dec 13 2014

last: Krook

address: von Eulers väg 4a

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

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


title: Dynamic time course mRNA profiling of human skeletal muscle cell differentiation.

summary:
The purpose of this study was to determine the miRNA expression profile of in vitro differentiation of human skeletal muscle cells and to couple changes in individual miRNA expression to effects on target genes by transcriptome profiling of mRNA expression.
mRNA expression profiling at three different time points during the in vitro differentiation process of human skeletal muscle cells from three subjects. RNA was harvested from myoblasts before and 4 and 10 days after induction of differentiation.

overall_design: Temporal, time-course design with paired analysis (3 subjects). Biological replicates: 3 at day 0, 3 at day 4, and 3 at day 10. One replicate per array.


title: Transcriptome Analysis of the Human Corneal Endothelium

status: Public on Nov 12 2014

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

summary:
Defining the normal and age-dependent HCEnC transcriptome will further refine our understanding of the functional roles that the endothelium plays in the cornea and will provide a basis upon which to compare transcriptomes of normal and dystrophic endothelium for the subsequent development of gene-targeted therapies.
We used microarrays to comprehensively characterize human corneal endothelial cell (HCEnC) gene expression, age-dependent differential gene expression and to identify expressed genes mapped to chromosomal loci associated with the corneal endothelial dystrophies PPCD1, FECD4 and XECD

overall_design: Eleven corneas from six pediatric (4, 6, 10,11, 17 and 18 years old) and five adult (53, 56, 57, 64 and 70 years old) donors, were obtained from various eye banks . Descemet and corneal endothelium were removed from donor eye bank corneas as intact sheets utilizing a technique that we have adapted for ex vivo donor tissue. Total RNA was isolated from the corneal endothelium using TriReagent and subsequently purified with the RNeasy Clean-Up Kit.  The integrity of the isolated RNA was analyzed using the Agilent 2100 Electrophoresis Bioanalyzer System  and found to be of sufficient quantity (approximately 1ug) and quality (RNA integrity number in the range of 8.3 to 9.0) for analysis using the Affymetrix 1.1ST gene chip arrays.

first: Ricardo

middle: F

last: Frausto

first: Cynthia


title: Impact of ulaR delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of ascorbic acid

status: Public on Oct 28 2014

department: MTC

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ∆ulaR  to D39 wild-type grown in M17 medium + 10mM ascorbic acid (AM17)

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

first: Muhammad

last: Afzal

first: Oscar

last: Kuipers


title: Mastermind-like protein 1 regulates DNA methylation and expression of early developmental gene clusters in human embryonic kidney cells (expression)

status: Public on Oct 08 2014

city: Huddinge

first: Milica

last: Putnik

address: Hälsovägen 7

department: Biosciences and Nutrition

institute: Karolinska Institute

summary:
Mastermind-like 1 (MAML1) is a transcriptional coregulator that has been associated with early development of many systems such as neuronal, muscular, cardiovascular and urogenital. The present study aimed to explore the genome-wide effects of MAML1 on gene expression and DNA methylation in human embryonic kidney cells. RNA expression was measured using a microarray that screens approximately 36,000 transcripts, and DNA methylation was determined for 450,000 CpG sites. 225 genes were found to be differentially expressed, while 11802 CpG sites were found to be differentially methylated in MAML1-expressing cells. A subset of 211 differentially methylated loci was associated with the expression of 85 genes. Gene ontology analysis revealed that these genes are involved in the regulation of urogenital system development, cell adhesion and embryogenesis.
The aim of the study was to identify genes regulated by mastermind-like pritein 1 and DNA methylation, using genome-wide approach.

overall_design: We assayed the effects of MAML1 overexpression, as well as knock-down, on global gene expression profiles in HEK293 cells. We applied a filter of p < 0.01 for significantly modulated gene expression and at least a 1.5-fold change in mean  differential expression. By comparing HEK293 (AW01-03_H average) with HEK293_MAML1 samples (AW04-06_MAML1 average), 225 genes were found to be differentially expressed. However, no significant changes were observed by comparing HEK293_H_siControl (AW13-14_H_siCtrl average) with HEK293_H_siMAML1 (AW15-16_siMAML1 average).

first: David

last: Brodin

first: Fredrik

last: Fagerström-Billai

first: Karin

last: Dahlman-Wright

first: Annika

middle: E

last: Wallberg


title: Human liver gene expression data from subjects of varying ages

status: Public on Nov 03 2014

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary: N=134 human liver samples from morbidly obese patients and healthy controls were analysed by array-based mRNA expression profiling. Liver messenger RNA expression datasets from the German patients were generated on the HuGene 1.1 ST gene array The purpose of the study was to correlate these gene expression data with body mass index and with an epigenetic measure of age acceleration based on DNA methylation data.

overall_design: The liver samples come from subjects whose body mass index ranged from 14.8 to 70.2.  Ages varied between 10 and 85.

first: Jochen

last: Hampe


title: Genome-wide analysis of basal gene expression in pediatric acute lymphoblastic leukemia xenograft cells

status: Public on Oct 02 2014

city: Sydney

first: Santi

last: Suryani

state: NSW

address: Level 5 Lowy Cancer Research Centre Gate 9 High St

department: Leukaemia Biology

country: Australia

institute: Children's Cancer Institute Australia for Medical Research

summary: Analysis of basal gene expression in patient-derived xenograft cells. A panel of pediatric T-, B- and MLL-ALL xenografts was utilized to further understand the biology of leukemia

overall_design: Total RNA was isolated from patient-derived xenograft cells. Array analysis was carried out on Illumina beadchip HT12

first: Richard

middle: B

last: Lock

first: Carol

last: Hernan

first: Sarmah

last: Chintanu

first: Suryani

last: Santi

first: Laura

last: High


title: Identification and characterization of androgen responsive biomarker genes in zebrafish embryos

status: Public on Sep 30 2014

city: Leipzig

first: Eva

last: Fetter

address: Permoserstraße 15

department: Bioanalytical Ecotoxicology

institute: UFZ-Helmholtz Centre for Environmental Research

summary: Exposure experiments with the non-aromatizable fish androgen, 11-ketotestosterone in the range of 0.05-5000 nM were conducted in order to identify potential androgen-responsive genes in zebrafish embryos by microarray analysis. Zebrafish embryos were treated from 96 hpf to 120 hpf in a single experiment with three controls (embryonic medium). Microarray studies were performed using a Custom 8x60k Gene Expression Microarrays (Amadid G4102A, based on the ensembl zebrafish genome version 3) from total RNA with low input labelling and hybridization kit (Agilent Technologies) and one-color design according to the manufacturer instructions. Fluorescent intensities of individual microarray spots were extracted using the Agilent Feature Extraction software. Raw microarray data were converted to log2 values and quantile-normalized. For further statistical analysis, fold changes in relation to the mean of the controls were calculated for each treatment.

overall_design: Zebrafish embryos were treated from 96 hpf to 120 hpf in a single experiment with three controls and 11 concentrations of 11-ketotestosterone ranging from 0.05-5000 nM.

first: Stefan

last: Scholz


title: Expression data from activated NK cells [RNA]

status: Public on Sep 09 2014

city: montpellier

first: martin

last: villalba

address: CHU Montpellier Hôpital Saint-Eloi 80, av. Augustin Fliche.

department: INSERM U1040

institute: Institut for Research in Biotherapy of Montpellier

summary:
Natural Killer (NK) cells present natural cytotoxicity against tumor cells, although their activity is increased after activation. NK cell activation depends on a complex intracellular signaling process mediated by activating and inhibitory receptors and the functional outcome depends on the integration of the activating and inhibitory signals received. Soluble cytokines and/or ligands on target cells bind the NK cell receptors, and hence, influence the final NK cell response: attack versus ignorance.
We used microarrays to detail the global programme of gene expression underlying NK cell activation by IL-2, a MHC-I-deficient target cell (K562)+IL-2 and an EBV-target cell (R69).

overall_design: PBLs from 4 different donors were activated by 100 U/ml IL-2; K562+IL-2 or R69 cells. After 5 days we obtained RNA and miRNA from naïve NK cells or from NK cells activated with the above mentioned stimuli, with more than 90% of purity. The 16 RNA samples were used to generate cDNA libraries that were hybridized on Human Gene 1.1ST arrays (Affymetrix) and analyzed with the Affymetrix Gene Chip Command Console Software v3.0 (AGCC 3.0, Affymetrix®) and the Expression Console Software v1.1 (Affymetrix®).

first: Martin

last: Villalba

first: Julian

last: Pardo


title: iPS from healthy control and BMPR2 mutant

status: Public on Aug 04 2014

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary: Comparison between inducible pluripotent stem cells from healthy patients and patients with BMPR2 mutation, at different differentiation stages.

overall_design: two arrays per differentiation stage; two genotypes; four differentiation stages

first: Susan

last: Majka


title: Glucosamine profiling of lymphocyte derived cell lines

status: Public on Aug 18 2014

city: Porto

first: Rune

last: Matthiesen

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

summary: Define regulated genes upon 24 hours of glucosamine treatment in KMH2 and Ramos

overall_design: A total of 8 samples were analysed. 6 samples constitute three biological replicas of KMH2 before and after 24 hours of glucosamine treatment. 2 samples are before and after 24 hours of glucosamine treatment of Ramos cell line.

first: Ana

middle: S

last: Carvalho Matthiesen


title: Gene expression profiles of PDX models with acquired resistance to endocrine treatments

status: Public on Jul 09 2014

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Acquired resistance to endocrine therapy occurs with high frequency in patients with luminal breast cancer (LBC). We report here the establishment of four patient-derived xenograft models of LBC with acquired resistance in vivo to tamoxifen and estrogen deprivation.

overall_design: CEL files represent expresison data generated from 5 replicates (independent mice) of the following tumor models: HBCx22 (parental), HBCx22 TamR (tamoxifen-resistant), HBCx22 OvaR (ovariectomy-resistant), HBCx34 (parental), HBCx34 TamR (tamoxifen-resistant), HBCx34 OvaR (ovariectomy-resistant)

first: Elisabetta

last: Marangoni


title: Influence of dietary fatty acid composition on white adipose tissue gene expression in humans

status: Public on Jul 01 2014

first: Ingrid

last: Dahlman

summary:
In a randomized controlled dietary intervention study, we compared a diet enriched in polyunsaturated fatty acids (PUFA) with a diet enriched in saturated fatty acids (SFA) for influence on abdominal subcutaneous adipose tissue gene expression. We studied young lean adults; 11 women and 25 men. There was no significant difference in age, BMI, or gene expression between the PUFA and SFA groups before the intervention. The intervention lasted for seven weeks.
We calculated for each gene the absolute difference in gene expression after vs. before intervention (deltas), and compared the deltas between the PUFA and SFA group using SAM. 12 genes were significantly differentially regulated by the two diets with a FDR of 25%. These include metabolic and adipokine genes. In conclusion, dietary fatty acids have a modest influence on white adipose tissue gene expression.

overall_design: Abdominal subcutaneous adipose needle biopsies were obtained from young adults before (W0) and after completion (W7) of the dietary intervention. From the biopsies we extracted RNA. From total RNA we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.1 ST Arrays (Affymetrix, Inc., Santa Clara, CA), and then washed, stained and scanned the slides using standardised protocols (Affymetrix, Inc.). Signicance analysis of microarrays (SAM) was use to compare the difference in gene expression between groups.

first: Ulf

last: Riserus


title: Expression data from human dental follicle cells

status: Public on Aug 01 2014

city: Regensburg

first: Sandra

last: Viale Bouroncle

address: Franz-Josef-Strauß-Allee 11

institute: University Hospital Regensburg

summary: We analysed the genexpression of dental follicle cells (DFCs) after 3 days osteogenic differentiation with BMP2 after transfection with a DLX3 plasmid (pDLX3) and after transfection with an empty plasmid (pEV)

overall_design: Total RNAs were isolated from dental follicle cells after transfection with pDLX3 and pEV and osteogenic induction with BMP2 at day 3

last: Viale-Bouroncle

first: Christian

last: Morszceck


title: Impact of lacR delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Glucose

status: Public on Jun 20 2014

first: Sulman

last: Shafeeq

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔlacR to D39 wild-type grown in M17 medium + 0.5 % (w/v) Glucose (GM17).

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

first: Muhammad

last: Afzal

first: Oscar

last: Kuipers


title: Transcriptional response of Streptococcus pneumoniae D39 to Lactose

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in M17 medium + 0.5 % (w/v) Lactose (LM17) to grown in M17 medium + 0.5 % (w/v) Glucose (GM17).

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


title: Impact of lacT delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Lactose

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔlacT to D39 wild-type grown in M17 medium + 0.5 % (w/v) Lactose (LM17).


title: Transcriptional response of Streptococcus pneumoniae D39 to Galactose

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in M17 medium + 0.5 % (w/v) Galactose (GaM17) to grown in M17 medium + 0.5 % (w/v) Glucose (GM17).


title: Effect of Notch1 pathway activation on high-grade glioma cells

status: Public on Jun 04 2014

city: MOntpellier

first: jean-philippe

last: hugnot

state: languedoc

address: IGF INSERM UM 141 rue de la cardonille

institute: inserm inm u1191

summary:
In this study, we explored the transcriptomic consequences of strong activation of the Notch pathway in embryonic human neural stem cells and in gliomas. For this we used a forced expression of the Notch intracellular domain (NICD).

Glioblastoma multiforms (GBMs) are highly vascularized brain tumors containing a subpopulation of multipotent cancer stem cells. These cells closely interact with endothelial cells in neurovascular niches. In this study we have uncovered a close link between the Notch1 pathway and the tumoral vascularization process of GBM stem cells. We observed that although the Notch1 receptor was activated, the typical target proteins (HES5, HEY1, HEY2) were not or barely expressed in two explored GBM stem cell cultures. Notch1 signalling activation by expression of the intracellular form (NICD) in these cells was found to reduce their growth rate and migration which was accompanied by the sharp reduction of neural stem cell transcription factor expression (ASCL1, OLIG2, SOX2) while HEY1/2, KLF9, SNAI2 transcription factors were upregulated. Expression of OLIG2 and growth were restored after termination of Notch1 stimulation.  Remarkably, NICD expression induced the expression of pericyte cell markers (NG2, PDGFRb and a-smooth muscle actin (aSMA)) in GBM stem cells. This was paralleled with the induction of several angiogenesis-related factors most notably cytokines (HB-EGF, IL8, PLGF), metalloprotease (MMP9) and adhesion proteins (VCAM-1, ICAM-1, ITGA9). In xenotransplantation experiments, contrasting with the infiltrative and poorly-vascularized tumors obtained with control GBM stem cells, Notch1 stimulation resulted in poorly-disseminating but highly-vascularized grafts containing large vessels with lumen. Notch1-stimulated GBM cells expressed pericyte cell markers and closely associated with endothelial cells. These results reveal an important role for the Notch1 pathway in regulating GBM stem cell plasticity and angiogenic properties.

overall_design: Embryonic human neural progenitors obtained from Lonza, the U87 glioma cell line, and glioma cancer stem cells (Gb4 and Gb7) characterized in Guichet et al. (Glia, 2013, 61(2), 225-39) were infected with lentiviruses expressing YFP or YFP-IRES-NICD (activated form of Notch receptor). After 48h, RNA were extracted for Affymetrix microarray analysis.

first: Jean

last: Hugnot

middle: O

last: Guichet

first: Bernard

last: Rothhut


title: Large-Scale Gene Expression Profiling of Developing Soybean Seeds of Evans

status: Public on Sep 11 2014

city: Ames

first: Ling

last: Li

state: IA

address: 443 Bessey Hall

department: Department of Genetics, Development, and Cell Biology

institute: Iowa State University

summary:
Developing Evans seeds at 25, 30, 40, 45 and 50 days after flowering (DAF) were harvested and analyzed to gain insights as to the biochemical program that determines soybean seed development.
We used microarrays to detail the global programme of gene expression underlying seed development and identified distinct classes of genes with changed expression during this process.

overall_design: Sampled developing Evans seeds at 25, 30, 40, 45 and 50 days after flowering (5 time points), with two replicates each.

first: Eve

last: Wurtele


title: The role of the transcription factors LacR and LacT in the regulation of the lactose and galactose utilization pathways in Streptococcus pneumoniae

summary:
Transcriptome comparison of the Streptococcus pneumoniae strain D39 grown in the presence of either lactose or galactose with that of the strain grown in the presence of glucose, revealed the elevated expression of various genes and operons, including the lac gene cluster that is organized into two operons i.e. lac operon-I (lacABCD) and lac operon-II (lacTFEG). Deletion of the DeoR family transcriptional regulator lacR that is present downstream of the lac gene cluster, revealed elevated expression of lac operon-I, even in the absence of lactose. This suggests a function of LacR as a transcriptional repressor of lac operon-I that encodes enzymes involved in the Tagatose-6-P pathway in the absence of lactose or galactose. Deletion of lacR did not affect the expression of lac operon-II that encodes for a lactose-specific PTS. This finding was further confirmed by ?-galactosidase assays with PlacA-lacZ and PlacT-lacZ in the presence of either lactose or glucose as a sole carbon source in the medium. This suggests the presence of another transcriptional regulator in the regulation of lac operon-II, which could be the BglG-family transcriptional antiterminator LacT. We demonstrate the role of LacT as a transcriptional activator of lac operon-II in the presence of lactose and CcpA-independent regulation of the lac gene cluster in S. pneumoniae.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Insights into the invasiveness of triple negative breast cancer from genome-wide profiling of transcription factor AP-1 (expression)

status: Public on Jun 30 2014

city: Stockholm

first: Chunyan

last: Zhao

address: Hälsovägen 7-9

summary: Triple negative breast cancer (TNBC) is an aggressive clinical phenotype, and accounts for 15% to 20% of all breast cancers. The molecular determinants of malignant cell behaviors in TNBC remain largely unknown. We find that the AP-1 transcription factor component, Fra-1, is overexpressed in basal-like breast tumors, and its expression level has high prognostic significance. Depletion of Fra-1 or its heterodimeric partner c-Jun inhibits the proliferative and invasive phenotypes in TNBC cells. To gain insights into the transcriptional regulatory networks of AP-1 in TNBC cells, we combine genome-wide ChIP-seq with loss-of-function transcriptome analyses. We observe dysregulation of direct targets of the Fra-1/c-Jun heterodimer involved in cell proliferation, cell adhesion, and cell-cell contact. Intriguingly, we find that AP-1 mediates downregulation of E-cadherin through direct transcriptional induction of ZEB2. This work sheds light on the mechanisms and pathways by which TNBC acquires invasiveness and proliferative propensity.

overall_design: BT549 cells grown in complete medium were transfected with a control siRNA, siRNA targeting Fra-1 or siRNA targeting c-Jun for 72 h, and then global gene expression profiles were assessed. Three or four biological replicates were used for each group.

first: Yichun

last: Qiao

first: Karin

last: Dahlman-Wright

first: Philip

last: Jonsson

first: Cecilia

last: Williams

first: Li

last: Xu

first: Indranil

last: Sinha


title: The inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent

status: Public on Apr 17 2014

first: Hayrettin

last: Guven

address: Nobels Vag 16

summary: Clone (Whirly) of human BJhTERT (human foreskin cell line) cells exposed to PC3 mRFP cells

overall_design: Clones (Whirly) of human BJhTERT (human foreskin cell line) cells exposed to PC3 mRFP cells were analyzed with Affymetrix Whole Target (WT) Assay (GeneTitan plate format Gene ST 1.1)

first: David

last: Brodin


title: Aging-induced differential methylation in human PBMCs occurs with but often without change in expression of the associated gene (Expression)

status: Public on May 09 2014

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Aging is a progressive process that results in the accumulation of intra- and extracellular alterations that in turn contribute to a reduction in health. Age-related changes in DNA methylation have been reported before and may be responsible for aging-induced changes in gene expression, although a causal relationship has yet to be shown. Using genome-wide assays, we analyzed age-induced changes in DNA methylation and their effect on gene expression with and without transient induction with the synthetic transcription modulating agent WY14,643. To demonstrate feasibility of the approach, we isolated peripheral blood mononucleated cells (PBMCs) from five young and five old healthy male volunteers and cultured them with or without WY14,643. Infinium 450K BeadChip and Affymetrix Human Gene 1.1 ST expression array analysis revealed significant differential methylation of at least 5 % (ΔYO > 5 %) at 10,625 CpG sites between young and old subjects, but only a subset of the associated genes were also differentially expressed. Age-related differential methylation of previously reported epigenetic biomarkers of aging including ELOVL2, FHL2, PENK, and KLF14 was confirmed in our study, but these genes did not display an age-related change in gene expression in PBMCs. Bioinformatic analysis revealed that differentially methylated genes that lack an age-related expression change predominantly represent genes involved in carcinogenesis and developmental processes, and expression of most of these genes were silenced in PBMCs. No changes in DNA methylation were found in genes displaying transiently induced changes in gene expression. In conclusion, aging-induced differential methylation often targets developmental genes and occurs mostly without change in gene expression.

overall_design: Peripheral blood mononuclear cells were isolated from 10 volunteers (5 young 5 old), treated with the synthetic PPARalpha agonists WY14,643 or control for 13 hrs, and subjected to genome-wide DNA methylation and gene expression analysis. This entry contains the gene expression data.

first: Wilma

last: Steegenga

first: Tiffany

last: Morris

first: Mark

last: Boekschoten

first: Michael

last: Müller


title: Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth

status: Public on May 01 2014

summary: Different fibroblast cells (eight in total) with different inhibitory capacity were analyzed and compared for their gene expression profile by whole genome microarray.

overall_design: Different fibroblast cells (eight in total) were analyzed with Affymetrix Whole Target (WT) Assay (GeneTitan plate format Gene ST 1.1) in order to find out gene expression differences.


title: Early B-cell Factor 1 Regulates Adipocyte Morphology and Lipolysis in White Adipose Tissue [expression profiling]

status: Public on May 22 2014

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

summary: To investgate the role of EBF1 in human adipocyte, we performed global expression profiling in human adipocytes transfected with siRNA targeting EBF1.

overall_design: Human adipocytes differentiated in vitro were transfected with siRNA targeting EBF1 or Non-targeting Control. The cells were incubated for approximately 48 hours upon which Total RNA were purified.  Gene expression profiling was performed using Affymetrix Human Gene 1.1 ST arrays (Affymetrix, Inc., Santa Clara, CA). Data were analyzed with packages available from Bioconductor (www.bioconductor.org). Normalization and calculation of gene expression was performed with the Robust Multichip Average expression measure using oligo package. Prior to further analysis, a non-specific filter was applied to include genes with expression signal >30 in at least 20% of all samples. A total of three independent transfection experiments were performed for the pre-adipocytes obtained from one donor. Same experiment were repeated with cells from another donor.

first: Hui

first: Niklas

last: Mejhert

first: Mikael

last: Rydén

first: Peter

last: Arner


title: Combinatorial flexibility of cytokine during Human T helper cells differentiation

status: Public on May 29 2014

city: PAris

first: Maxime

last: Touzot

address: 26 rue d'ULM

institute: Institut Curie

summary: Transcriptional analysis of human T cells differentiated in 4 T Helper context ( Th0, Th1, Th2 and Th17) in the presence or not of Interferon alpha

overall_design:
We analyzed the transcriptomic profiles of 4 human naives T cells diferentiated in Th0, Th1, Th2 and Th17 in the presence or not of Interferon Alpha.
Microarray analyses were performed in 2 time points : 1/ after Day 5 of polarization (= Day5); 2/ after Day 5+ four hours of re-stimulation (=Day 5+ 4H restim)   in 3 different donors.

first: Maximilien

last: Grandclaudon

first: Antonio

last: Cappuccio

first: Takeshi

last: Satoh

first: Carolina

last: Martinez-Cingolani

first: Nicolas

last: Servant

last: Manel

first: Vassili

last: Soumelis


title: Functional Genomics of miR-2909 in HeLa229 cells.

status: Public on Mar 05 2014

city: Chandigarh

first: Deepak

last: Kaul

state: Chandigarh

address: Sec 12

department: Experimental Medicine & Biotechnology

institute: PGIMER

summary: Since HeLa229 cells were found unable to express miR-2909 gene expression in their native state, these cells were used as archetype model to explore the functional genomics of miR-2909.

overall_design: HeLa229 cells were transfected with either control vector or miR-2909 expression vector and subsequently these cells were incubated in RPMI-1640 nutrient medium for 48 hrs at 37°C in 5% CO2 atmosphere. At the end of this incubation period the cells from each well were processed for RNA isolation followed by microarray analysis of the effector genes.

first: A

last: Raina

first: Anuradha

last: Garg


title: Global gene expression induced by CP1020 (Cyanopeptolin) in zebrafish eleuthero-embryo (Danio rerio)

status: Public on Mar 31 2014

city: Muttenz

first: Susanne

last: Faltermann

address: Gründenstrasse 40

department: IEC

country: Switzerland

institute: Fachhochschule Nordwestschweiz

summary:
Cyanobacteria produce various cyanotoxins, which can cause severe effects to other organisms. Microcystins, one group of such toxins, primarily produced by species of Microcystis, are strong hepatotoxins and inhibit potently protein phosphatases 1 and 2A. Microcystin is the most studied cyanotoxin, however, others are not investigated. Eutrophication of water bodies promotes the occurrence of toxic algal blooms and since a anthropogenic caused increase in eutrophication events can be observed, it is becoming increasingly important to study the consequences and to increase the knowledge on toxins associated with algal blooms.
Recently a new cyanobacteria toxin from a Microcystis strain, CP1020, was described. CP1020 belongs to the class of cyanopeptolins and its toxicity was shown to be comparable to that of microcystin (Gademann et al., 2009). It is a strong protease inhibitor inhibiting trypsin in the picomolar range (IC50 = 670 pM) and effects survival of the freshwater crustacean Thamnocephalus platyurus (LC50) 8.8 μM (Gademann et al., 2009). Nothing is known, however, about the toxicity of CP1020 to fish. Furthermore, no information is available on the toxic modes of action, in addition to the proteinase activity. Consequently our study has the aim to elucidate the modes of action of CP1020 on zebrafish eleuthero-embryos. By using a microarray technique, we will analyse alterations of global gene expression by CP1020 at two different concentrations. Thereby, we hope to elucidate the whole array of affected biological pathways to elucidate the mechanisms by which CP1020 affect fish.

overall_design: Gene expression in zebrafish eleuthero-embryos was measured after exposure for 96h to 100 ug/L and 1000 ug/L CP1020 or to the respective controls. A total of 12 arrays (Agilent 4 × 44 K Zebrafish microarray) were used, including four for the solvent control group, four for the 100 μg/L and four for the 1000 μg/L CP1020 dose group.

first: Sara

last: Zucchi

first: Esther

last: Kohler

first: Judith

last: Blom

first: Jakob

last: Pernthaler

first: Karl

last: Fent


title: Increased Rho GTPase activity is associated with decreased tumor inhibitory activity of immortalized fibroblasts

status: Public on Mar 08 2014

first: Tatiana

last: Pavlova

address: Nobelsvag 16

institute: Karolinska Institutet

summary: Two clones (Whirly and Crossy) of human BJhTERT (human foreskin cell line) cells with different inhibitory capacity were analyzed and compared for their gene expression profile by whole genome microarray.

overall_design: Two clones (Whirly and Crossy) of human BJhTERT (human foreskin cell line) cells were analyzed with Affymetrix Whole Target (WT) Assay (GeneTitan plate format Gene ST 1.1) in order to find out gene expression differences.

first: Hayrettin

last: Guven

first: David

last: Brodin


title: Effects of miR-106a~363 blocking sponge on Sk-ES-1 Ewing Sarcoma Cell line Gene Expression Profile

status: Public on Dec 01 2013

city: Aurora

first: Layne

last: Dylla

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary: The objective of this study was to determine the effects of miR-106a~363 blockade on the gene expression profile of Ewing Sarcoma cell lines (Sk-ES-1 cells)

overall_design: Microarray analysis was performed on 3 samples from Sk-ES-1 cells stably expressing the control CXCR4 miRNA sponge and 3 samples from Sk-ES-1 cells stably expressing the miR-106a~363 cluster blocking miRNA sponge

first: Paul

last: Jedlicka


title: Genome-wide gene expression during osteogenic and myogenic differentiation from adipose- derived stem cells.

status: Public on Oct 03 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: In the current study, we have performed a gene expression analysis of well characterized and defined populations of human adipose-derived stem cells (hASCs) before and after in vitro induction of osteogenic and myogenic differentiation that allows identifying DNA methylation- regulated differentiation genes. We have also address the extent of the epigenetic programming of hASCs- derived differentiated cells by comparing the expression profiling of these cells with their somatic counterparts from primary tissues. Finally, we also compared the patterns of expression of hASCs (and their derivatives)

overall_design: Identify all genes or probe-sets whose expression was significantly different between control hASCs and each one of the two differentiated cell types (DIF.M and DIF.O),

first: María

last: Berdasco


title: Alterations in the transcriptome of soybean in response to enhanced somatic embryogenesis promoted by 35S:GmAGL15

status: Public on Jan 30 2014

city: Lexington

first: Sharyn

last: Perry

state: KY

address: 1405 Veterans Dr.

department: Plant and Soil Sciences

institute: University of Kentucky

summary:
A soybean ortholog of the Arabidopsis MADS-domain transcription factor (called GmAGL15) enhanced somatic embryogenesis from immature cotyledon explants of soybean when expressed via the 35S promoter compared to non transgenic tissue (cultivar Jack). To better understand how this occurs an expression microarray experiment was performed.
publication: Q. Zheng and S.E. Perry. (2014). Alterations in the transcriptome of soybean in response to enhance somatic embryogenesis promoted by orthologs of AGAMOUS-Like 15 and AGAMOUS-Like 18. Plant Physiology, in press.

overall_design: Comparison of transcriptomes of non-transgenic tissue to 35S:GmAGL15 tissue at the time of explant preparation (0 days) and 3 and 7 days after induction of somatic embryogenesis by placement on medium containing 2,4-D.

first: Qiaolin

last: Zheng


title: Effects of 30 days resveratrol supplementation on adipose tissue morphology and gene expression patterns in obese men

status: Public on Sep 25 2013

first: Guido

last: Hooiveld

summary: Polyphenolic compounds, such as resveratrol, have recently received widespread interest due to their ability to mimic effects of calorie restriction. The objective of the present study was to gain more insight into the effects of 30 days resveratrol supplementation on adipose tissue morphology and underlying processes. Nine healthy obese men were supplemented with placebo and 150mg/day resveratrol for 30 days, separated by a 4-week washout period. A postprandial abdominal subcutaneous adipose tissue biopsy was collected to assess adipose tissue morphology and gene expression using microarray analysis. Resveratrol significantly decreased adipocyte size, with a shift towards a reduction in the proportion of large and very large adipocytes and an increase in small adipocytes. Microarray analysis revealed downregulation of Wnt, Notch and BMP/TGF-β signaling pathways and upregulation of pathways involved in cell cycle after resveratrol supplementation, suggesting enhanced adipogenesis. Furthermore, the lysosomal/phagosomal pathway and the transcription factor EB were upregulated, reflecting an alternative pathway of lipid breakdown by autophagy. These data suggest that adipose tissue is an important target tissue for the effects of resveratrol in humans, but further research is necessary to investigate whether it translates into an improved adipose tissue function.

overall_design: In a double-blind randomized crossover study, 9 healthy obese men were supplemented with placebo and 150 mg/day resveratrol for 30 days, with a 4-week washout period in between. At the end of each intervention period, a biopsy was taken from the abdominal subcutaneous adipose tissue, which was subjected to gene expression profiling.

first: Ellen

last: Konings

first: Silvie

last: Timmers

first: Mark

last: Boekschoten

first: Gijs

last: Goossens

first: Johan

middle: W

last: Jocken

first: Lydia

middle: A

last: Afman

first: Michael

last: Müller

first: Patrick

last: Schrauwen

first: Edwin

middle: C

last: Mariman

last: Blaak


title: Gene expression changes induced by LKB1 expression in human lung adenocarcinoma cell lines

status: Public on Oct 01 2013

city: Columbus

first: David

last: Carbone

state: Ohio

address: 460 West 12th Avenue; 488 BRT

department: Internal Medicine

institute: Ohio State University

summary:
LKB1 is a tumor suppressor lost in approximately 30% of lung adenocarcinomas. It is a serine-threonine kinase involved in regulating metabolism, proliferation, and cell polarity. We have characterized its association with mRNA expression profiles in resected tumors and in cell lines, but little is known about the direct effects of LKB1 on the regulation of these genes.
This study investigates the effects of LKB1 activity on mRNA expression in two LKB1-mutant lung adenocarcinoma cell lines, H2122 and A549. Wild-type LKB1 has been stably expressed in these cell lines using a pBABE retrovirus as well as an empty pBABE control and a kinase-dead mutant of LKB1 (K78I) control (Addgene). Samples submitted are two cell lines, three experimental conditions, and three replicates, for a total of 17 samples (one sample was excluded for poor RNA quality). Gene expression of these samples are analyzed to determine transcriptional regulatory effects of LKB1 expression. Results of this analysis are compared to our analysis of resected human tumors to determine gene patterns that are differentially expressed between LKB1-deficient and LKB1-wild-type tumors whose expression is also affected by restoration of LKB1 in vitro.

overall_design: RMA gene expression was taken from two cell lines stably expressing LKB1 or controls of K78I mutant LKB1 or empty pBABE vector. Log2 average expression differences are calculated and compared to results from analysis of gene expression associated with LKB1 loss in resected human tumors.

first: Carbone

last: David

first: Kaufman

last: Jacob


title: Gene expression profiling of MDA231, BT549, and SUM159PT cells after selumetinib treatment or DUSP4 siRNA knockdown

status: Public on Sep 03 2013

first: Justin

middle: M

last: Balko

address: 777 Preston Research Building

summary: MDA231, BT549, and SUM159PT basal-like breast cancer cell lines were transfected with non-targeting siRNA (siCONTROL), siRNA targeting DUSP4 (siDUSP4), or siCONTROL + 4 or 24 hr of 1uM selumetinib.  Cells were harvested at 96 hr post-siRNA transfection.  Data were Log2 RMA normalized.

overall_design: We sought to identify changes in gene expression after MEK inhibition, or after loss of DUSP4 function in breast cancer cell lines.

first: Carlos

middle: L

last: Arteaga


title: Evolution of monoclonal zebrafish Myc-induced T-ALL, assessed by copy number variant analysis

status: Public on Jan 29 2014

city: Charlestown

last: Langenau

state: MA

institute: Massachusetts General Hospital

type: Genome variation profiling by genome tiling array

summary: Clonal evolution and intratumoral heterogeneity drive cancer progression through unknown molecular mechanisms. To address this issue, functional differences between single T-cell acute lymphoblastic leukemia (T-ALL) clones were assessed using a zebrafish transgenic model. Functional variation was observed within individual clones, with a minority of clones enhancing growth rate and leukemia propagating potential with time. We analyzed CNVs between monoclonal primary transplants and secondary transplants of clones that evovled increased leukemia propagating potential, and well as non-evovled clones with inherently high and low leukemia propagating potential. The goal of this study was to identify CNVs commonly assoicated with increased leukemia propagating cell frequency.

overall_design: Myc-induced T-ALL were generated in syngenic CG1. Single T-ALL cells were transplanted into recipitent CG1, resulting in monoclonal T-ALL.  In some instances, the monoclonal T-ALL were serially passaged. Leukemia propagating frequency was calculated for each T-ALL clone, at each passage. In this analysis, 9 primary T-ALL and 35 monoclonal T-ALL were individually run against a CG1 control.

first: Jessica

last: Blackburn

first: Sali

last: Liu

first: Jayme

last: Wilder

first: Kimberly

last: Dobrinski

first: Riadh

last: Lobbardi

first: Finola

last: Moore

first: Sarah

last: Martinez

first: Eleanor

middle: Y

last: Chen

first: Charles

last: Lee


title: Early molecular assessment of osseointegration in humans

status: Public on Sep 17 2013

city: Chapel Hill

first: Lyndon

last: Cooper

state: NC

address: 330 Brauer Hall, CB#7450

department: Prosthodontics

institute: UNC School of Dentistry

summary: To determine the early temporal wide genome transcription regulation by the surface topography at the bone-implant interface of implants bearing micro-roughened or superimposed nanosurface topology.

overall_design: Fourty four cp titanium implants with surface topographies exhibiting nanoscale features (Osseospeed-OS) and microrough surface without nanoscale features (TiOblast-TiO) were placed in the alveolar bone of 11 systemically healthy subjects and subsequently harvested at 3 and 7 days after placement. Total RNA was isolated from cells adherent to retrieved implants. A whole genome microarray using the Affymetrix Human gene 1.1 ST Array  was used to describe the gene expression profiles that were differentially regulated by the implant surfaces.

first: Ghadeer

middle: N

last: Thalji

first: Salvador

last: Nares


title: Human liver biopsy of different phases from control to NASH

status: Public on Aug 08 2013

first: Timo

last: Itzel

institute: Universitätsklinikum Regensburg

summary: Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients (N=45) with all stages of NAFLD and controls (N=18) were analysed by array-based DNA methylation and mRNA expression profiling. NAFLD-specific expression and methylation differences were seen for nine genes coding for key enzymes in intermediate metabolism (including PC, ACLY, PLCG1) and insulin/insulin-like signalling (including IGF1, IGFBP2, PRKCE) and replicated by bisulfite pyrosequening (independent N=39). Transcription factor binding sites at NAFLD-specific CpG sites were >1000-fold enriched for ZNF274, PGC1A and SREBP2. Intra-individual comparison of liver biopsies before and after bariatric surgery showed NAFLD-associated methylation changes to be partially reversible. Post-bariatric and NAFLD-specific methylation signatures were clearly distinct both in gene-ontology and transcription factor binding site analyses, with >400-fold enrichment of NRF1, HSF1 and ESRRA sites. Our findings provide one of the first examples of treatment-induced epigenetic organ remodelling in humans.

overall_design: 73 samples of human liver grouped into C (control=14), H (healthy obese=27), S (steatosis=14) and N (nash=18).

first: Hampe

last: Jochen

first: Teufel

last: Andreas

first: Itzel

last: Timo


title: Gene expression profiles of dental follicle cells after seven days of ostoeogenic differentiation

status: Public on Jul 19 2013

first: Oliver

last: Felthaus

address: Franz-Josef-Strauss-Allee 11

department: Department of Cranio- and Maxillofacial Surgery

summary: We analysed gene expression profiles in dental follicle cells after seven days of ostoeogenic differentiation

overall_design: Total RNAs were isolated from dental stem cells at day 0 (before differentiation) and after 7 days of differentiation)

first: Martin

last: Gosau

first: Christian

last: Morsczeck