title: Analysis of RNA Based Transcriptome of Mycobacterium leprae genome from Environmental and Clinical Samples

type: Expression profiling by genome tiling array

summary:
BACKGROUND: This study was conducted to analyse M. leprae gene expression profiles in biopsy of leprosy patient and in environmental soil samples. Investigation was carried out to find out the expression profile for the minimal gene set necessary for growth of environmental M. leprae and its genes potentially require for infection and pathogenesis of leprosy.
METHOD: RNA was extracted from human biopsy and environmental soil samples and total RNA obtained by subtractive hybridization of rRNA, was reverse transcribed and amplified using random primers. The whole genome was tiled at 10bp to obtain probes having 60 mer oligonucleotides in sense orientation. 179963 probes were designed in both sense and antisense orientation. Blast was performed against the mRNA sequence databases to check the specificity of the probes. Finally, 359926 probes were designed and 56579 specific probes were replicated to fill the remaining spots.
RESULTS: Up regulation of several functional genes of M. leprae genome were observed from soil samples responsible for metabolism of Carbon compounds [9], Amino acids and amines [4] , Fatty acids synthesis [21], Lipid Biosynthesis [33], Phosphorous compounds [2]. Up regulation of genes were observed from soil samples in energy metabolism function such as Glycolysis [6], Pyruvate dehydrogenase [1], TCA cycle [12], Glyoxylate bypass [12]. In up regulation of respiration function [11] genes were observed and some of genes responsible for miscellaneous oxidoreductases and oxygenases [22] function, ATP-proton motive force [4] were also observed. Up regulation of genes for cell envelope function [65], conserved membrane proteins [107], cell processes [62], central intermediary metabolism [79], polyamine synthesis[38], biosynthesis of cofactors, prosthetic groups and carriers [36], broad regulatory functions [35], macromolecule metabolism[103], degradation of macromolecules [25], miscellaneous transferases [36], conserved hypothetical [204] and unknowns  [101] were observed.  Significant up regulation of Virulence genes [9], PE and PPE families [3] were also observed from soil samples.
CONCLUSION: Transcriptome analysis indicated that up regulation of essential genes of M. leprae transcripts in environmental samples as compared to M. leprae from human biopsy samples which strongly suggested that several M. leprae genes are expressed more in environment for its survival and may act as source of infection.

first: Ravindra

middle: P

last: Turankar

first: Ishangi

last: Agrawal

first: Mallika

last: Lavania

first: Itu

last: Astha Nigam

first: Joydeepa

last: Darlong

first: Mohamed

last: Aiyaz

first: Utpal


title: Coordinated activities of EZH2 and EZH1 are essential for neurogenesis

status: Public on May 24 2016

city: Barcelona

first: Conchi

last: EI

address: Baldiri Reixac 15

country: Spain

institute: IBMB

summary: Polycomb group proteins (PcG) are well known by their function in the regulation of developmental processes. PcG mediated regulation of genetic programs required for proper development are triggered by EZH2 H3K27 methyltransferase activity. EZH1 can partially substitute EZH2 activity. However, unlike EZH2, EZH1 is presence in differentiated and adult tissues suggesting additional biological functions. Here we show that EZH2 is predominantly expressed in neural stem cells being essential for neural stem cells self renewal and homeostasis. There, it controls the transcriptional state of cell cycle regulators, such as CIP1. But it is also necessary to regulate genes involved in surveillance and neuroepithelial polarity. In contrast, EZH1 expression is more abundant in differentiated cells within the spinal cord and its downregulation unables neural stem cells to differentiate. All together our data reveal a complementary but non-redundant role of EZH2 and EZH1 in neurogenesis.

overall_design: In order to understand how EZH2 might regulate neurogenesis in chick embryo spinal cord cells we performed a transcriptional profiling of flow cytometry purified GFP+ neuroblasts from shRNA-EZH2 or shRNA-Control electroporated neural tubes. Specifically, electroporated embryos were dissected out 48h after electroporation and trypsinized for 5-10 min in 0.5% Trypsin-EDTA (Sigma). Trypsinization was stopped by 20% horse serum in PBS-0.1% glucose solution. GFP+ cells from cell suspension were sorted by flow cytometry using a MoFlo flow cytometer (DakoCytomation, Fort Collins, CO). mRNA from GFP positive cells from dissected shRNA-control or shRNA-EZH2 electroporated neural tubes was extracted by TRIZOL (Invitrogen) protocol with 2   l of pellet paint co-precipitant (Novagene). Then, RNA was processed to hybridization on Affymetrix microarrays.

first: Alejandra

last: García


title: Transcription profiling of 8 months and 24 months old rat radial and sciatic nerves

status: Public on May 12 2016

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

summary:
The objective of this study was to determine which pathways are significantly regulated with age in sciatic and radial nerves, individually or considering the interaction term.
We find a strong signature of the cholesterol biosynthesis pathway being downregulated with age in both nerves, however, this effect is significantly milder in the radial nerve.

overall_design: We collected both radial and sciatic nerves from 8 adult (8 months old) and 8 old (24 months old) rats.

first: Alice

last: Pannérec

first: Eugenia

last: Migliavacca

first: Sylviane

last: Métairon

first: Frédéric

last: Raymond

middle: N


title: Comparison of gene expression in M. tuberculosis TrxB2-DUC mutant treated or not with atc

city: NEW YORK

first: Kan

last: Lin

state: New York

address: 413 East 69th Street

department: Microbiology and Immunology

country: USA

institute: Weill Cornell Medical College

summary: M. tuberculosis thioredoxin reductase (TrxB2) is essential for bacterial survival in vitro and in vivo. To gain insight into the mechanisms underlying lethality caused by TrxB2 depletion, we compared the mRNA profiles of TrxB2-DUC mutant in the presence and absence of atc.

overall_design: We grew bacteria in 7H9 medium to an OD of 0.5~0.6 and then added atc to a final concentration of 400ng/ml. Samples were collected 6 h and 24 h after atc treatment.

first: Sabine

last: Ehrt


title: Comparison of gene expression in M. tuberculosis TrxB2-DUC mutant treated or not with atc and DTT

summary: M. tuberculosis thioredoxin reductase (TrxB2) is essential for bacterial survival in vitro and in vivo. To gain insight into the pathways dependent on TrxB2, we compared the mRNA profiles of TrxB2-DUC mutant in the presence and absence of atc and DTT.

overall_design: We grew bacteria in 7H9 medium to an OD of 0.5~0.6. We then added atc to a final concentration of 800 ng/ml and DTT to a final concentration of 2 mM. Samples were collected 24 hr after treatment.


title: Transcriptional profiling of arabidopsis plants

status: Public on Jun 01 2016

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: au13-08_atpplaii-alpha - transcriptional profilling of arabidopsis plants. Understanding the physiological role of pPLAIIα; under control and drought stress conditions. Study on empty vector, overexpressor and antisense A. thaliana lines.

overall_design: 6 dye-swap - genotype comparison, treated vs untreated

first: Christian

last: Meyer

first: Ana-Rita

last: Matos

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Comparison of gene expression in M. tuberculosis TrxB2 mutants

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

overall_design: Refer to individual Series


title: Transcriptomic study in RNA pol II foot mutants

status: Public on Mar 31 2016

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: The goal of the project was to study the effects on transctiptome of some Rpb1 foot mutations that block Rpb4/7 assembly

overall_design: Cells were grown in YPD at 30ºC to 0.5 OD600. At that cells were spun-down or changed to 37ºC by adding hot YPD. These aliquots were cultured for 30 min and collected. Thus, wt and mutants have two samples: 30 and 37ºC. Each sample was done in triplicate.

first: José

middle: E

last: Pérez-Ortín

first: Ana

middle: I

last: Garrido-Godino

last: García-Martínez

first: Francisco

last: Navarro


title: Comparison of gene expression in M. tuberculosis TrxB2-TetON-tetO-WT mutant treated or not with atc

summary: M. tuberculosis thioredoxin reductase (TrxB2) is essential for Mtb physiology and pathogenesis. To gain insight into its biological functions, we generated the TrxB2-TetON-tetO mutants, in which TrxB2 is partially depleted in the absence of atc without impairing bacterial viability.

overall_design: We grew TrxB2-TetON-tetO-WT in 7H9 medium with 400 ng/ml atc, until the OD reached 0.5~0.6. Then Mtb was washed with 7H9 medium 3 times and suspended in 7H9 medium with or without atc. Then samples were taken 24, 48, 72 and 120 hrs later.


title: Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [array]

status: Public on Mar 28 2016

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: RNA binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNAs. As defects in protein-RNA recognition lead to human disease, UV-crosslinking and immunoprecipitation (CLIP) of ribonuclear complexes followed by deep sequencing (-seq) is critical in constructing protein-RNA maps to expand our understanding of RBP function. However, current CLIP protocols are technically demanding and involve low complexity libraries that yield squandered sequencing of PCR duplicates and high experimental failure rates. To enable truly large-scale implementation of CLIP-seq, we have developed an enhanced CLIP methodology (eCLIP) that features a decrease of ~10 cycles of requisite amplification with a concomitant >60% decrease in discarded PCR duplicate reads, while maintaining the ability to identify RNA binding with single-nucleotide resolution. By simplifying the generation of paired IgG and size-matched input controls, eCLIP also dramatically improves specificity in discovery of authentic binding sites. To demonstrate that eCLIP enables large-scale and robust profiling of RBPs, 102 eCLIP experiments in biological duplicate for a diverse collection of 74 RBPs in HepG2 and K562 cells were completed (available at https://www.encodeproject.org). We establish that eCLIP is comparable in amplification and sample requirements to ChIP-seq, and enables integrative analysis of diverse RBPs to reveal factor-specific profiles, common artifacts for CLIP experiments and RNA-centric perspectives of RBP activity.

overall_design: Microarray profiling of RBFOX2 knockdown by shRNAs in 293T cells

first: Eric

last: Van Nostrand

first: Gabriel

middle: A

last: Pratt

first: Alexander

last: Shishkin

first: Chelsea

last: Gelboin-Burkhart

first: Mark

last: Fang

first: Balaj

last: Sundararaman

first: Steven

last: Blue

first: Thai

last: Nguyen

first: Christine

last: Surka

first: Keri

last: Elkins

first: Rebecca

last: Stanton

first: Frank

last: Rigo

first: Mitchell

last: Guttman


title: 24-epibrassinolide regulates the expression of miRNAs in Arabidopsis thaliana

status: Public on Mar 25 2016

city: Taipei

first: Hsueh-Fen

last: Juan

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

department: institute of molecular and cellular biology

country: Taiwan

institute: National Taiwan university

summary: Brassinosteroids (BRs) are endogenous plant hormones and essential for normal plant growth and development. MicroRNAs (miRNAs) of Arabidopsis thaliana are involved in mediating cell proliferation in leaves, stress tolerance, and root development. The specifics of BRs mechanisms involving miRNAs are unknown. To explore the role of miRNAs in BR-mediated pathways, we analyzed differences in miRNA profiles between control (mock solution) and 24-epibrassinolide (EBR) treatments from customized miRNA microarrays.

overall_design: Seedlings were separately cultured under exogenous 10 nM EBR treatments for 30 (EBR30) or 180 (EBR180) minutes, and total RNAs of all seedlings were extracted after seven days of growth. Two independent experiments were performed at each time (30 or 180 minutes).

first: Li-Ling

last: Lin

first: Chia-Chi

last: Wu

first: Hsuan-Chang

last: Huang

first: Huai-Ju

last: Chen

first: Hsu-Liang

last: Hsieh


title: Host response to systemic bacterial challenge (sepsis) with E. coli strains CFT073 and F11 at 6 and 12 hours post inoculum

status: Public on Mar 29 2016

city: Jena

first: Amelia

last: Barber

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Fungal Informatics

country: Germany

institute: Leibniz-HKI

overall_design: 48 hpf embryos were manually dechorianated, briefly anesthetized with 0.77 mM ethyl 3-aminobenzoate methanesulfonate salt (tricaine) (Sigma-Aldrich), and embedded in 0.8% low melt agarose (MO BIO Laboratories) without tricaine. After the agarose solidified, embryos were immersed in E3 media lacking methylene blue. Prior to injection, 1 ml of bacterial culture was pelleted, washed with 1 ml sterile PBS, and re-suspended in PBS to obtain ~1X109 CFU/ml. PBS. One nl of this bacterial suspension containing  ~1000 CFU was microinjected into the bloodstream via the circulation valley using an Olympus SZ61 or SZX10 stereomicroscope together with a YOU-1 micromanipulator (Narishige), a Narishige IM-200 microinjector, and a JUN-AIR model 3-compressor. For each experiment, the average CFU per injection was determined by adding 10 1-nl drops to 1 ml of 0.7% NaCl, which was then serial diluted and plated on Luria-Bertani (LB) agar plates. Mock-infected controls were inoculated with 1 nl sterile PBS.  Following injection, embryos were removed from agar and placed individually into wells of a 48-well plate (Nunc) containing E3 medium and incubated at 28.5°C. Experiments were performed in biological quadruplicate.

first: Matthew

last: Mulvey


title: Boolean modeling reveals the necessity of transcriptional regulation for bistablity in PC12 Cell Differentiation

status: Public on Mar 23 2016

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: The nerve growth factor NGF has been shown to cause cell fate decisions towards either differentiation or proliferation depending on the relative activity of downstream pERK, pAKT or pJNK signaling. However, how these protein signals are translated into and fed back from transcriptional activity to complete cellular differentiation over a time span of hours to days is still an open question.  Using dynamic proteome and transcriptome data from NGF-stimulated PC12 cells over a time span of 24 hours we inferred a dynamic Boolean model capturing the temporal sequence of protein signaling, transcriptional response and subsequent autocrine feedback. Optimal model topology was achieved by introducing multiple time scales for fast cellular signaling and slower gene response and subsequent fitting to the experimental data.  The integrated model confirmed the parallel use of MEK/ERK, AKT/PI3K and JNK/JUN for PC12 cell differentiation. Redundancy of cell signaling is demonstrated from the inhibition of the different MAPK pathways. As suggested in silico and confirmed in vitro, differentiation was substantially suppressed under JNK/JUN inhibition, yet delayed only under MEK/ERK inhibition. Most importantly, we found that sustained transcriptional feedback is necessary to induce bistability in the cell fate switch. De novo Gene expression was necessary to activate autocrine feedback that caused integrin signaling to perpetuate the MAPK activity, finally resulting in the expression of late, differentiation related genes. Thus, the cellular decision towards differentiation depends on the establishment of a transcriptome-induced positive feedback between protein signaling and gene expression thereby constituting a robust control between proliferation and differentiation.

overall_design: To eludicate the transcriptome response of PC12 cells time-resolved gene expression data of NGF or EGF simulated PC12 were recorded at t = [0.5h 1h, 2h, 3h, 4h, 5h, 6h, 8h, 12h, 24h, 48h] for NGF and at t=[1h, 2h, 3h, 4h, 6h, 8h, 12h, 24h]. Control time points of unstimulated PC12 cells were taken at t=[0h, 2h, 4h, 6h, 8h, 24h, 48h]. Additionally, the MEK-inhibitor UO126 was added together with NGF and the gene response was measured at t=[1h, 2h, 4h, 6h, 8h, 12h, 24h, 48h] and for UO126 alone at t=[1h, 2h, 4h, 8h, 12h, 48h]. Total RNA was isolated, labeled and hybridized to an Illumina ratRef-12 bead array  (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

first: Melanie

last: Boerries

first: Sebastian

last: Weber

first: Maria

last: Fernandez-Cachon

first: Barbara

last: Offermann

first: Amit

last: Singh


title: Chromosome-wide DNA unmethylome profiling examining human chromosomes 2, 9, 19 and mouse chromosomes 1, 9, 19

city: Toronto

first: Arturas

last: Petronis

address: 250 College St Rm606

country: Canada

institute: Centre for Addiction and Mental Health

type: Methylation profiling by genome tiling array

summary: The unmodified DNA fraction of jejunal enterocytes and the jejunum lacking enterocytes of humans and jejunal enterocytes of mice was interrogated on Affymetrix tiling arrays

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The mTAG technique was used to enrich the unmodified DNA fraction in a total of 56 humans and 26 mice

first: Art

first: Viviane

last: Labrie

first: Orion

middle: J

last: Buske


title: Genome-wide mapping of Hif-1α binding sites in zebrafish [microarray]

status: Public on Mar 22 2016

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

summary: Analysis of gene expression changes in the von Hippel Lindau when mutant compared to wild-type at 4dpf using a whole genome microarray expression profiling. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. We performed single-colour microarrays to identify the gene expression changes which underpin the hypoxic phenotype.  We used 3 biological replicates from both mutant and control, followed by analysis using Limma to identify significant gene expression changes. This work, together with ChIP-seq data for the Hif-1α in von Hippel Lindau mutants, should allow for the Hif-1α dependency  of these gene expression changes to be assessed.

overall_design: The changes in gene expression between von Hippel Lindau mutants and wild-type controls was measured at 4 days post fertilisation. For both wild-type and mutant, 3 biological replicates, each of 30 embryos were used.

first: David

last: Greenald

last: Jeyakani

first: Bernd

last: Pelster

first: Ian

last: Sealy

first: Sinnakaruppan

last: Mathavan

first: Fredericus

last: van Eeden


title: Inhibition of Medulloblastoma growth by a sonic hedgehog (SHH) inhibitor

status: Public on Mar 14 2016

city: Roma

first: Gessica

last: Filocamo

address: Via Savona 6

country: Italy

institute: Exiris s.r.l.

summary:
Aberrant activation of the Hedgehog (Hh) signaling pathway is implicated in the pathogenesis of many cancers, including medulloblastoma and basal cell carcinoma (BCC). In this study, using neonatally irradiated Ptch1+/- mice as a model of Hh-dependent tumors, we investigated the in vivo effects of MK-4101, a novel SMO antagonist, for treatment of medulloblastoma and BCC. Results clearly demonstrate a robust antitumor activity of MK-4101, achieved through the inhibition of proliferation and induction of extensive apoptosis in tumor cells. Of note, beside antitumor activity on transplanted tumors, MK-4101 was highly efficacious against primary medulloblastoma and BCC developing in the cerebellum and skin of Ptch1+/- mice. By identifying the changes induced by MK-4101 in gene expression profiles in tumors, we also elucidate the mechanism of action of this novel, orally administrable compound. MK-4101 targets the Hh pathway in the tumor cells, showing the maximum inhibitory effect on Gli1 activity.
MK-4101 also induced deregulation of cell cycle and block of DNA replication in tumors. Members of the IGF and Wnt signaling pathways , were among the most highly deregulated genes by MK-4101, suggesting that the interplay among Hh, IGF and Wnt is crucial in Hh-dependent tumorigenesis. Altogether, the results of this preclinical study support a therapeutic opportunity for MK-4101 in the treatment of Hh-driven cancers, also providing useful information for combination therapy with drugs targeting pathways cooperating with Hh oncogenic activity.

overall_design: Gene expression data was generated (in replicates) from Medulloblastoma allografts collected at various time points and following low (40mpk) or high (80 mpk) or vehicle single dose (QD) or mutiple dose (BID) treatment with a SHH pathway inhibitor.

first: Mirko

last: Brunetti

first: Fabrizio

last: Colaceci

first: Romina

last: Sasso

first: Mirella

last: Tanori

first: Emanuela

last: Pasquali

first: Mariateresa

last: Mancuso

first: Anna

last: Saran

first: Armin

last: Lahm

first: Christian

last: Steinkühler

first: Simonetta

last: Pazzaglia


title: Oscillating profiles of global genes in Synechocystis sp. PCC 6803 in diurnal light/dark cyles.

city: St. Louis

first: Himadri

last: Pakrasi

state: Missouri

address: One Brookings Dr.

department: Biology

institute: Washington University in St. Louis

summary: RNA samples from cells collected at twenty four time points in 48-hours diurnal cycles were analyzed, and they compared between each other for transcriptional profiles of global genes

overall_design: 24 RNA samples at different time points will be compared for this cycling condition. An equimolar mixture of RNA from all time points was used as the control.

first: Rajib

last: Saha

first: Deng

last: Liu


title: ChIP-chip data of HA-Yra1 and Rrm3-Flag in wild-type and cells overexpressing YRA1

status: Public on Mar 11 2016

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

type: Genome binding/occupancy profiling by genome tiling array

summary:
Transcription is a major obstacle for replication fork progression and a cause of genome instability. Yra1 is an essential nuclear factor of the evolutionarily conserved family of hnRNP-like export factors that when overexpressed impairs mRNA export and cell growth.
Through this ChIP-chip analysis it is shown that Yra1 binds to active chromatin and is enriched at telomeres when it is overexpressed, in agreement with a possible role of this mRNP factor in the maintenance of telomere integrity. Our data indicate that YRA1 overexpression correlates with replication impairment as inferred by the increase of Rrm3, a helicase involved in the replication fork progression, at transcribed genes and telomeres.

overall_design: ChIP-chip studies were perfomed with antibodies against HA-tagged Yra1 protein in wild-type cells and cells overexpressing YRA1 of the yeast S. Cerevisiae, as well as Flag-tagged Rrm3 protein in both wild-type and cells overexpressing YRA1.

first: Sandra

last: Gavaldá

first: José

middle: M

last: Santos-Pereira

first: María

middle: L

last: García-Rubio

first: Rosa

last: Luna


title: Gene Expression profiling and pathway analysis in MCF-7 and MDA-MB-231 human breast cancer cell lines treated with dioscin

city: University

first: Asok

middle: K

last: Dasmahapatra

state: MS

address: 313 Faser Hall

department: National Center for Natural Product Research

institute: University of Mississippi

summary: The long-term goal of our study is to understand the genetic and epigenetic mechanisms of breast cancer metastasis in human and to discover new possible genetic markers for use in clinical practice. We have used microarray technology (Human OneArray microarray, phylanxbiotech.com) to compare gene expression profiles of non-invasive MCF-7 and invasive MDA-MB-231 cells exposed to dioscin (DS), a steroidal saponin isolated from the roots of wild yam, (Dioscorea villosa). Initially the differential expression of genes (DEG) was identified that followed pathway enrichment analysis (PEA). Of the genes queried on OneArray, we identified 4641 DEG changed between MCF-7 and MDA-MB-231 cells (vehicle-treated) with cut-off log2 |fold change|≧ 1. Among these genes, 2439 genes are upregulated and 2002 genes are downregulated. DS exposure (2.30 M, 72 h) to these cells identified 801 (MCF-7) and 96 (MDA-MB-231) DEG that showed significant difference compared to untreated cells (p<0.05). Within these gene sets, DS is able to upregulate 395 genes and downregulate 406 genes in MCF-7 and upregulate 36 and downregulate 60 genes in MDA-MB-231 cells.  Further comparison of DEG between MCF-7 and MDA-MB-231 cells exposed to DS identified 3626 DEG of which 1700 were upregulated and 1926 genes were down-regulated. From PEA, 12 canonical pathways were significantly altered between these two cell lines (MCF-7 and MDA-MB-231). However, no alteration in any of these pathways was noticed in MCF-7 cell, while in MDA-MB-231 cells only MAPK pathway showed significant alteration. When PEA comparison was made on DS exposed cells, it was observed that only 2 pathways were significantly affected. Further, to identify shared DEG, which are targeted by DS and overlapped in both MCF-7 and MDA-MB-231 cells, we performed intersection analysis (Venn diagram). We found that only 7 DEG are overlapped of which six are reported in the database. This study highlights the diverse gene networks and pathways through which DS exhibits its effect on breast cancer cells.

overall_design: Two condition experiment. Human breast cancer Cell line MCF-7 groups: Vehicle control and dioscin treated; Human breast cancer cell line MDA-MB-231 cell group; vehicle control and dioscin-treated. Biological replicates: MCF-7 control compared to MCF-7 dioscin treated; MDA-MB-231 control compated to MDA-MB-231 dioscin-treated; MCF-7 control compared to MDA-MB-231 control; MCF-7 dioscin treated compared to MDA-MB-231 dioscin-treated. duplicate array

first: Pranapda

last: Aumsuwan

first: Shabana

last: Khan

first: Ikhlas

first: Larry

last: Walker


title: Treatment of MM cells with IMiDs or reducing the expression of EIF2C2 significantly affects steady-state levels of miRNAs

status: Public on Mar 09 2016

city: scottsdale

first: qinqin

last: xu

state: arizona

address: 13400 E shea blvd

institute: mayo clinic arizona

summary: Lenalidomide is a therapeutically active compound that binds to E3 ubiquitin ligase recruiter cereblon (CRBN) and induces cytotoxicity. We have identified eukaryotic translation initiation factor 2 subunit C2 (EIF2C2) as a new member of CRBN-downstream binding protein that plays an important role in microRNA (miRNA) maturation and function. The treatment of immunomodulatory drug (IMiD)-sensitive multiple myeloma (MM) cells with lenalidomide altered the steady-state levels of CRBN, EIF2C2 and miRNAs and induced apoptosis. However, although the treatment of IMiD-resistant MM cells with lenalidomide altered the steady-state levels of CRBN, EIF2C2 and miRNAs, but did not massively induce apoptosis. In contrast, silencing of EIF2C2 with its small hairpin RNA significantly altered the levels of miRNAs and induced apoptosis regardless of whether those cells are sensitive or resistant to IMiDs. Therefore, EIF2C2 could be considered as a new drug target for overcoming IMiDs resistance in MM cells.

overall_design: To find the role of EIF2C2 in MM cell growth, OCI-My5 cell lines My5/LV and My5/CRBN, with low and high CRBN expression, respectively, were treated 12 different ways. The steady-state levels of miRNAs between (1) My5/LV, EIF2C2-shRNA-treated My5/LV and EIF2C2-cDNA-treated My5/LV cells, (2) My5/CRBN, EIF2C2-shRNA-treated My5/CRBN and EIF2C2-cDNA-treated My5/CRBN cells, (3) My5/LV cells, My5/LV cells treated with 10 µM lenalidomide for 72 hours or 120 hours, and EIF2C2-cDNA-treated My5/LV cells treated with 10 µM lenalidomide for 72 hours, and (4) My5/CRBN cells, My5/CRBN cells treated with 10 µM lenalidomide for 72 hours or 120 hours, and EIF2C2-cDNA-treated My5/CRBN cells treated with 10 µM lenalidomide for 72 hours, were compared in this array.

first: Qinqin

last: Xu

first: Xiubao

last: Chang


title: Genetic Manipulation of Putrescine Biosynthesis Reprograms the Cellular Transcriptome and the Metabolome

status: Public on Mar 24 2016

city: Huntsville

first: Leland

middle: J.

last: Cseke

state: AL

address: 301 Sparkman Dr.

department: Biological Sciences

institute: The University of Alabama Huntsville

summary:
Background: With the increasing interest in metabolic engineering of plants using various genetic manipulation and gene editing technologies in order to enhance their growth, nutritional value and environmental adaptation, a major concern is the potential of broad and distant effects of manipulating the target gene or the metabolic step in the resulting plant. A comprehensive transcriptomic and metabolomic analysis of the product may shed some useful light in this regard. The present study used these techniques with plant cell cultures to analyze the effects of genetic manipulation of a single step in the biosynthesis of polyamines because of their well-known roles in plant growth, development and stress responses [PMID 19383098]
The transcriptomes and metabolomes of a control and a high putrescine producing (HP) cell line of poplar (Populus nigra x maximowiczii) were compared using microarrays and GC/MS. The HP cells expressed an ornithine decarboxylase transgene and accumulated several-fold higher concentrations of putrescine, with only small changes in spermidine and spermine. The results show that up-regulation of a single step in the polyamine biosynthetic pathway (i.e. ornithine→putrescine) altered the expression of a broad spectrum of genes; many of them were involved in transcription, translation, membrane transport, osmoregulation, shock/stress/wounding, and cell wall metabolism. More than half of the 200 detected metabolites were significantly altered (P <0.05) in the HP cells on any day of analysis; the most noteworthy differences were in organic acids, carbohydrates and nitrogen-containing metabolites.  The results provide valuable information about the role of polyamines in regulating nitrogen and carbon use pathways in cell cultures of high putrescine producing transgenic cells of poplar vs. their low putrescine counterparts. The results underscore the complexity of cellular responses to genetic perturbation of a single metabolic step related to nitrogen metabolism in plants. Combined with recent studies from our lab regarding increased putrescine production causing an increased flux of glutamate into ornithine, with accompanied increase in glutamate production by additional nitrogen and carbon assimilation; the results may be useful in designing transgenic plants with increased nitrogen use efficiency, especially in plants intended for non-food/feed applications (e.g. increased biomass production or for biofuels).

platform_organism:
Populus trichocarpa x Populus deltoides
Populus euphratica
Populus tremula x Populus alba

overall_design:
12 two-channel arrays directly comparing RNA from control and high putrescine producing (HP) cell lines of Populus nigra x maximowiczii at 3 and 5 days of growth.  Three independent biological replicates derived from cells grown in three independent replicate cultures were used.  In addition, each sample and time point included dye swap reciprocal two-color experiments for each biological replicate. Thus, six data points per cDNA are included (three biological replicates with two technical replicates each).

Please note that experiments were technically carried out as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array; barcode ID for each array is indicated in the sample title and raw data file names) but two idependent raw data files were generated from each slide (one for Cy3, the other for Cy5) and processed as though they are single channel (Cy3 and Cy5 signals are calculated and provided for each sample record). Therfore, each sample record is represented as single channel sample.

first: Andrew

middle: F

last: Page

first: Rakesh

last: Minocha

first: Swathi

last: Turlapati

first: Gopi

last: Podila

first: Alexander

last: Ulanov

first: Zhong

last: Li

first: Subhash

middle: C


title: Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation: genotyping data for the identification of mQTL

status: Public on Mar 21 2016

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

summary: Haplotype-dependent allele-specific methylation (hap-ASM) can impact disease susceptibility, but maps of this phenomenon using stringent criteria in disease-relevant tissues remain sparse. Here we apply array-based and Methyl-seq approaches to multiple human tissues and cell types, including brain, purified neurons and glia, T lymphocytes, and placenta, and identify 795 hap-ASM differentially methylated regions (DMRs) and 3,082 strong methylation quantitative trait loci (mQTLs), most not previously reported. More than half of these DMRs have cell type-restricted ASM, and among them are 188 hap-ASM DMRs and 933 mQTLs located near GWAS signals for immune and neurological disorders. Targeted bis-seq confirmed hap-ASM in 12/13 loci tested, including CCDC155, CD69, FRMD1, IRF1, KBTBD11, and S100A*-ILF2, associated with immune phenotypes, MYT1L, PTPRN2,CMTM8 and CELF2, associated with neurological disorders, NGFR and HLA-DRB6, associated with both immunological and brain disorders, and ZFP57, a trans-acting regulator of genomic imprinting. Polymorphic CTCF and transcription factor (TF) binding sites are over-represented among hap-ASM DMRs and mQTLs, and analysis of the human data, supplemented by cross-species comparisons to Macaca mulattamacaques, indicates that CTCF and TF binding likelihood predicts the strength and direction of the allelic methylation asymmetry. These results show that hap-ASM is highly tissue-specific; an important trans-acting regulator of genomic imprinting is regulated by this phenomenon; variation in CTCF and TF binding sites is an underlying mechanism in primary tissues, and maps of hap-ASM and mQTLs reveal regulatory sequences underlying supera- and sub-threshold GWAS peaks in immunological and neurological disorders.

overall_design: Genomic DNA from 54 T cells,  47  brains (temporal cortex) and 37 fetal placentas were hybridized to the Illumina HumanOmni2.5-8v1.1 (Omni2.5) BeadChip. Illumina HumanOmni2.5 arrays were performed by the Genomics Shared Resource supported by Roswell Park Cancer Institute and National Cancer Institute (NCI). Sample-dependent and sample-independent controls were evaluated to ensure the reagent performance, efficiency of hybridization and the staining process as well as to evaluate sample quality and performance.  Each SNP was analyzed independently to identify genotypes. Genotypes were called by comparing generated data with those in a standard cluster file.  To identify mQTL (methylation quantitative trait loci), these genotyping data were used in combination with methylation data obtained using  Illumina Infinium 450k Human Methylation Beadchip arrays.

first: Catherine

last: Do

first: Charles

last: Lang

first: John

last: Lin

first: Huferesh

last: Darbary

first: Izabela

last: Krupska

first: Aulona

last: Gaba

first: Lynn

last: Petukhova

first: Jean-Paul

last: Vonsattel

first: Mary

last: Gallagher

first: Robin

middle: S

last: Goland

first: Raphael

last: Clynes

last: Dwork

middle: G

last: Kral

last: Monk

first: Angela

last: Christiano


title: Dietary phytochemicals modulate skin gene expression and reduce lice counts after infection in Atlantic salmon

status: Public on Mar 19 2016

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: BACKGROUND: The use of phytochemicals is a promising solution in biological control against salmon louse (Lepeophtheirus salmonis). Glucosinolates (Gls) belong to a diverse group of compounds used as protection against herbivores by plants in the Brassicaceae family, while in vertebrates, ingested glucosinolates exert health-promoting effects due to their antioxidant and detoxifying properties as well as effects on cell proliferation and growth. The aim of this study was to investigate if Atlantic salmon fed two different doses of glucosinolate-enriched feeds would be protected against lice infection. The effects of feeding high dose of glucosinolates before the infection, and of high and low doses 5 weeks into the infection were studied.   METHODS: Skin was screened by 15k oligonucleotide microarray and qPCR.  RESULTS: 25% reduction (p < 0.05) in lice counts was obtained in the low dose group and 17% reduction in the high dose group compared to fish fed control feed. Microarray analysis revealed induction of over 50 interferon (IFN)-related genes prior to lice infection. Genes upregulated 5 weeks into the infection in glucosinolate-enriched dietary groups included Type 1 pro-inflammatory factors, antimicrobial and acute phase proteins, extracellular matrix remodeling proteases and iron homeostasis regulators. In contrast, genes involved in muscle contraction, lipid and glucose metabolism were found more highly expressed in the skin of infected control fish.   CONCLUSIONS: Atlantic salmon fed glucosinolates had a significantly lower number of sea lice at the end of the experimental challenge. Feeding glucosinolates coincided with increased expression of IFN-related genes, and higher expression profiles of Type 1 immune genes late into the infection. In addition, regulation of genes involved in the metabolism of iron, lipid and sugar suggested an interplay between metabolism of nutrients and mechanisms of resistance.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Atlantic salmon received feeds enriched in plant derived glucosinolates (Gls), with the approximate GLs content of 7.3 μmol/g and 26.4 μmol/g in the low dose group (LD) or the high dose group (HD), respectively.The treatment groups tested in this part of the study were named: infected C (I-C) infected LD (I-LD) and infected HD (I-HD), in three tank replicates. Skin samples were collected before infection and after 31-35 days of experimental lice infection. In addition, six tanks of fish were used in a parallel feed study to assess the effect of GLs feeding per se (without infection). These groups of fish were named not-infected high dose (NI-HD) and not-infected control (NI-C) respectively. Sampling of skin tissue was performed after 17-18 days of feeding using the same protocol as for the infected fish. Five individuals from each group were analyzed with microarrays, and 4 fish from NI-HD. Pooled skin samples of two salmon from each dietary group were used as a reference.

first: Jodaa

middle: H

last: Helle

first: Skugor

last: Stanko


title: Correlative Controls of Seeds over Maternal Growth and Senescence in Arabidopsis (expression)

status: Public on Mar 17 2016

city: Zurich

first: Samuel

middle: Elias

last: Wuest

address: Winterthurerstrasse 190

department: Institute of Evolutionary Biology and Environmental Studies

institute: University of Zurich

summary: Correlative controls (influences of one organ over another organ) of seeds over maternal growth are one of the most obvious phenotypic expressions of the trade-off between growth and reproduction. However, the underlying molecular mechanisms are largely unknown. Here, we characterize the physiological and molecular effects of correlative inhibition by seeds on Arabidopsis thaliana inflorescences, i.e. global proliferative arrest (GPA) during which all maternal growth ceases upon the production of a given number of seeds. We use laser-assisted microdissection and RNA-seq or Affymetrix GeneChip hybridizations to compare sterile growing, fertile growing and fertile arrested meristems or whole inflorescences. In shoot tissues, we detected the induction of stress- and senescence-related gene expression upon fruit production and GPA, and a drop in chlorophyll levels - suggestive of altered source-sink relationships between vegetative shoot and reproductive tissues. Levels of shoot reactive oxygen species, however, strongly decreased upon GPA - a phenomenon that is associated with bud dormancy in some perennials. Indeed, gene expression changes in arrested apical inflorescences after fruit removal resembled changes observed in axillary buds following release from apical dominance. This suggests that GPA represents a form of bud dormancy, and that dominance is gradually transferred from growing inflorescences to maturing seeds - allowing offspring control over maternal resources, simultaneously restricting offspring number.

overall_design: Examination of transcriptomes of four reproductive stages: i) sterile growing plants, ii) fertile growing plants, iii) fertile arrested plants, iv) arrested plants after removal of all fruits from the plant; includes whole inflorescences and laser-dissected shoot apices (meristematic regions)

first: S


title: Salinity induced gene expression profiling in 8 diverse rice genotypes

status: Public on Mar 10 2016

city: Mymensingh

first: Mohammad

middle: Rashed

last: Hossain

address: Factulty of Agriculture (East Building)

department: Genetics and Plant Breeding

country: Bangladesh

institute: Bangladesh Agricultural University

summary: Whole genome transcriptional responses is profiled in the 0 & 120 mM NaCl stressed whole seedlings of four indica (Pokkali, PSBRc50, IR 58, BRRI dhan 29), two Japonica (Banikat, Nipponbare) and two wild (O. latifolia, O. Rufipogon) accessions of rice (that showed varied level of tolerance to salt stresses) to identify the salinity induced transcripts. Stress was imposed on 14 day old seedlings and total RNA from the whole seedlings was collected after 48 h of stressed period (i.e., from 16 day old seedlings). These data sets were used for two different analyses. Firstly, the gene expression responses of eight rice genotypes was interrogated by the weighted continuous morpho-physiological trait responses (on a scale of 0 to 1) using a modified version of the ‘Significance Analysis of Microarrays’ (SAM) to identify the genes whose expression changes significantly and which is relative to the changes in morpho-physiological traits over these rice genotypes. Secondly, the differentially expressed significant salinity induced genes were also identified in the tolerant and in the susceptible genotypes using Gene-spring software. The genes that enriched the important biological processes and molecular functions (as identified by Gene Ontology: Singular enrichment analysis) are discussed in a way to explain the roles of these genes in overall stress adaptation mechanism.

overall_design: Fourteen day old whole seedlings of 8 rice genotypes were treated with 0 & 120 mM NaCl stress for 48 hours each with three replications and the gene expressions were measured using Agilent Rice Gene Expression 4x44K Microarray.

middle: R

first: Brian

middle: V

last: Ford-Lloyd


title: Transcriptome analysis of a Staphylococcus aureus mutant defective in the transcription termination factor Rho.

status: Public on Mar 08 2016

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

institute: INRAE - Université Paris-Saclay

summary:
This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (Mäder, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different
biological conditions. The data revealed a relatively low abundance of antisense RNAs in S. aureus, overlapping only 6% of the coding genes. Transcriptome analysis of the rho deletion mutant revealed a remarkable overall increase in antisense transcription in S. aureus.

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: delta rho and wild type

first: Ulrike

last: Mäder

first: Michel

last: Debarbouille

first: Cyprien

last: Guérin

first: Aurelia

last: Hiron

first: Magda

last: van der Kooi-Pol

first: Marc

last: Schaffer


title: Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions

summary: We report the condition-dependent transcriptome of S. aureus HG001, a derivative of strain NCTC 8325, by strand-specific tiling array hybridizations. More than 40 experimental conditions were investigated ranging from optimal in vitro growth to interaction with host cells. Analyses included the systematic mapping of transcription units, annotation of non-coding RNAs, the classification of promoters according to their dependency on SigA and SigB, and the prediction of potentially new transcription factor target sites. Antisense RNAs being of particular interest because of the small number of alternative sigma factors used by S. aureus were found to be relatively rare, overlapping only 6% of the annotated coding genes.

overall_design:
RNA samples prepared from S. aureus HG001 grown in shake flask or cell culture infection experiments were reverse transcribed, labeled and hybridized to tiling arrays.
Hybridizations were performed in triplicate using RNA isolated from independent cultures.

first: Maren

last: Depke

first: Jan

last: Pané-Farré

first: Ewoud

last: Reilman


title: Staphylococcus aureus HG001

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

overall_design: Refer to individual Series


title: Tiling array hybridizations of genomic DNA from Staphylococcus aureus HG001.

summary:
This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (Mäder, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different bilogical conditions.
Genomic DNA was prepared from four independent cultures of S. aureus HG001 cells; after sonication, DNA was labeled with Cy3 and hybridized to tiling arrays.
The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift.

overall_design: genomic DNA from wild type


title: Autoantibodies and nucleic acids skew complement consumption in systemic lupus erythematosus [C3]

status: Public on Mar 07 2016

city: Budapest

first: Krisztian

last: Papp

address: 1/C Pazmany P.

country: Hungary

institute: MTA-ELTE Immunology Research Group

summary: Systemic lupus erythematosus is a chronic autoimmune disease with multifactorial ethiopathogenesis. The complement system is involved in both the early and late stages of disease development and organ damage. To better understand autoantibody mediated complement consumption the GAPAID consortium examined ex vivo immune complex formation on autoantigen arrays.  We recruited patients with SLE (n=211), with other systemic autoimmune diseases (n=65) and non-autoimmune control subjects (n=149) in two rheumatology tertiary care centers. Standard clinical and laboratory data were collected from all subjects and serum complement levels were determined in SLE patients. The genotype of SNP rs1143679 in the ITGAM gene was also determined. On-chip formation of immune complexes was examined using a functional immunoassay on autoantigen microarray. The amount of antigen-bound IgM, IgG and complement C4 and C3 was quantified on autoantigens comprising nucleic acids, proteins and lipids.  Our results show that the relatively high complement consumption of nucleic acids is further increased upon binding of IgM and IgG. This is true even when serum complement levels are decreased due to complement consumption in SLE patients. A negative correlation between serum complement levels and ex vivo complement deposition on nucleic acid autoantigens is demonstrated. On the contrary, most protein and lipid autoantigens show positive correlation with C4 and C3 levels. Genetic analysis reveals that the non-synonymous variant rs1143679 in complement receptor type 3 is associated with an increased production of anti-dsDNA IgG antibodies. Notwithstanding, homozygous carriers of the previously reported susceptible allele (AA) have lower levels of dsDNA specific IgM among SLE patients. Regarding organ involvement we find that besides anti-C1q IgG, low levels of dsDNA specific IgM and low complement C4 binding to C1q are also associated with renal injury.  In summary, nucleic acids maintain a skewed complement deposition balance when bound by IgG and IgM, depleting the early classical complement pathway from other physiological processes. Dysfunction of the receptor responsible for complement-mediated apoptotic debris removal promotes the development of autoantibodies targeting nucleic acids. These observations provide serological and genetic evidence for complement-mediated clearance deficiency of apoptotic debris in lupus.

platform_organism:
Homo sapiens
Bos taurus
Capra hircus

overall_design: C3, IgM, C4 and IgG binding in 425 human serum samples were examined using custom-made protein arrays

first: József

last: Prechl

first: Zoltán

last: Herincs

first: Hajna

last: Peterfy

first: Lóránd

last: Veronika

last: Szittner

first: Del

last: Jokin

first: Uribarri

last: Maria

first: Rovero

last: Paolo

first: Andone

last: Estonba

first: Ilaria

last: Paolini

first: Paola

last: Migliorini

first: Otsanda

last: Larrañaga

first: Claudia

last: Alcaro

first: László

last: Czirjak


title: Autoantibodies and nucleic acids skew complement consumption in systemic lupus erythematosus [C4]


title: SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells [array]

city: San Francisco

first: Barbara

last: Panning

state: CALIFORNIA

address: 600, 16TH STREET, S374 - Genentech Hall,

department: Biochemistry and Molecular biology

institute: University of California, San Francisco

summary: The transcription factor SOX2 is central in establishing and maintaining pluripotency. The processes that modulate SOX2 activity to promote pluripotency are not well understood. Here, we show SOX2 is O-GlcNAc modified in its transactivation domain during reprogramming and in mouse embryonic stem cells (mESCs). Upon induction of differentiation SOX2 O-GlcNAcylation at serine 248 is decreased. Replacing wild type with an O-GlcNAc-deficient SOX2 (S248A) increases reprogramming efficiency. ESCs with O-GlcNAc-deficient SOX2 exhibit alterations in gene expression. This change correlates with altered protein-protein interactions and genomic occupancy of the O-GlcNAc-deficient SOX2 compared to wild type. In addition, SOX2 O-GlcNAcylation impairs the SOX2-PARP1 interaction, which has been shown to regulate ESC self-renewal. These findings show that SOX2 activity is modulated by O-GlcNAc modification, and provide a novel regulatory mechanism for this crucial pluripotency transcription factor.

overall_design: To determine if the fSOX2-Tg and fS248A-Tg mouse embryonic stem cell lines (mESC) exhibited differences in gene expression changes, we used microarrays to compare the transcriptomes of the two mESC lines. We had triplicate biological samples per mESC line.

first: Sailaja

last: Peddada

first: Samuel

last: Myers

first: Gregor

last: Krings


title: Autoantibodies and nucleic acids skew complement consumption in systemic lupus erythematosus [IgG]

first: Krisztian

last: Papp

first: József

last: Prechl

last: Herincs


title: Autoantibodies and nucleic acids skew complement consumption in systemic lupus erythematosus [IgM]

first: Zoltán

first: Hajna

last: Peterfy

last: Veronika

last: Szittner


title: Identification of Dpp target genes during the early embryo development

status: Public on Feb 24 2016

city: Santiago de Chile

first: Calixto

last: Dominguez

state: Región Metropolitana

address: Zanartu 1482

department: Center for Bioinformatics and Genome Biology

country: Chile

institute: Fundación Ciencia y Vida

summary: The dorsal patterning in Drosophila is controlled by an extracellular gradient of the morphogens Decapentlaplegic/Screw (Dpp/Scrw), which are members of BMP/TGF-β family. Dpp/Scrw signal is transduced to the nucleus by the transcription factors, Mad/Medea. The transcriptional effectors exert their regulation in a graded-manner eliciting at least three threshold responses: high, intermediate and low. However, the mechanism underlying differential response to Dpp is poorly understood, due in part to the insufficient number of well-studied target genes. Gene expression changes were analysed in ectopic overexpressing Dpp mutant embryos to identify new target genes of Dpp/Mad pathway.

overall_design: Total RNA from nos-Gal4>lacZ and nos-Gal4>Uas-dpp embryos (N=100-200) at stages 5 to 7 of development was extracted as described in Zuñiga et al. (BMC Biology. 7:61, 2009). The fluorophores Cy3 or Cy5 (Amersham) were coupled with aminoallyl-modified nucleotides after amplification of total RNA following manufacturer’s instructions (MessageAmp II aRNA Amplification Kit (Ambion, cat. AM1753). After purification, dye incorporation was calculated. Experimental and control labeled 2.5 μg of aRNA probes were co-hybridized to microarrays in a blocking solution. Glass slides with probe spots distributed in 48 blocks representing the Drosophila transcriptome were purchased from Microarrays Inc (http://www.microarrays.com/). Two independent control (nos-Gal4>lacZ) and experimental (nos-Gal4>UAS-dpp) embryos samples (biological replicates) were hybridized in nine slides to an oligonucleotide microarray (Microarray Inc.). The experimental and control samples were tagged with Cy5 and Cy3, respectively, three hybridizations were dye swapped. Slides were pre-hybridized, hybridized and washed according to recommendations of Microarray Inc. Images were processed using the software ScanArray Express (Perkin Elmer) to aligning both channels at different PTM gain. Image quality was assessed by descriptors included within the R function, q.com. Additionally, control spots (spike controls, empty spots and random oligomers) were analyzed separately to discriminate high quality hybridized slides. The data from selected slides were processed to remove noise with normexp, normalized by block with loess and to identify differentially expressed genes by using the statistical R package LIMMA. LIMMA is able to estimates the coefficients of the contrast matrix between the conditions and fits a linear model for each gene. Estimation of significance is based on a hypothesis test that uses the statistical t-moderate associated to p-value. P values were adjusted by the method of Benjamini and Hochberg to control the rate of false values. Genes with statistically significant changes in expression (adjusted P-value < 0.05) were selected.

first: Alejandro

last: Zuñiga

first: Patricia

last: Hanna

first: Christian

last: Hodar

first: Mauricio

last: Gonzalez

first: Verónica

last: Cambiazo


title: Gene expression profiling of Foxi3 null embryonic back skin epithelium

status: Public on Mar 01 2016

city: Helsinki

first: Vera

last: Shirokova

address: Viikinkaari 9

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary: Foxi3 is a transcription factor expressed in the hair follicle epithelium during development and postnatally. In this study we used a microarray analysis to indentify differentially expressed genes in Foxi3 null epithelium compared to Foxi3 wt epithelium. We used E15.5 stage as the earliest time point when the Foxi3 null hair phenotype bacame obvious, to find out the most early consequences of Foxi3 ablation.

overall_design: Dispase-dissociated back skin epithelia of 4 Foxi3 total null and 4 wild-type E15.5 mouse embryos, littermates from 4 litters of C57/Bl6 background, were used for the analysis. Array and data analysis were performed in the Biomedicum Functional Genomics Unit (University of Helsinki, Finland).

first: Marja

last: Mikkola


title: Common asymptomatic and submicroscopic malaria infections in Western Thailand revealed in longitudinal molecular and serological studies: a challenge to malaria elimination.

status: Public on Feb 01 2016

city: Irvine

first: Elisabeth

last: Baum

address: Med Surge II

institute: University of California Irvine

summary: Malaria is the most important vector-borne disease in Southeast Asia. In Thailand, malaria incidence has been in decline, with the annual parasite incidence dropping to 0.56 in 2007. The Myanmar-Thai border province of Tak is considered meso-endemic for malaria, and both Plasmodium vivax (Pv) and P. falciparum (Pf) are equally present. As part of the International Centers for Excellence in Malaria Research (ICEMR) - Southeast Asia project, malaria surveillance is conducted in Tak on both the healthy population and hospital patients, and parasite prevalence is reportedly <1%. However, little is known about the immuno-epidemiology associated with Pf and Pv infections in the region regarding the breadth and targets of the antibody response to the malaria parasites. Our hypothesis is that the serological profiles of the population will reflect the low parasite prevalence in Tak, showing little antibody reactivity to Pv and Pf. To examine this question, we developed a protein microarray displaying the top 500 most immunogenic antigens of these two Plasmodium species. We collected whole blood samples from healthy residents of Mae Salid Noi village during a Mass Blood Survey for malaria in the region. Whole blood was sent to UCI for qPCR and serology analysis. Blood plasma was probed on the protein microarray; genomic DNA was extracted from RBC pellets and screened by qPCR for infection confirmation and species identification. One-hundred percent (n=381) of serum samples were reactive to both Pv and Pf antigens, including all qPCR-negative samples.

platform_organism:
Plasmodium falciparum
Plasmodium vivax

overall_design: Antibody profiling against P. falciparum and P. vivax proteins was performed on sera from residents of Thailand's Tak province as part of Southeast Asia International Centers for Excellence in Malaria Research (ICEMR). Samples were collected during community-based surveys (n= 298) and hospital outpatient samples (n= 83) in March, August 2013 and January 2014; and 16 unexposed USA controls were probed on a protein microarray displaying 500 P. falciparum and 515 P. vivax proteins.

first: Jetsumon

last: Prachumsri

first: Jeeraphat

last: Sirichaisinthop

first: Aarti

last: Jain

first: Douglas

last: Molina

first: Xiaowu

last: Liang

first: Phillip

last: Felgner

first: Guiyun

last: Yan


title: Detection of a Yersinia pestis homologue in rodent samples

status: Public on Feb 11 2016

city: Loughborough

first: Tim

last: Giles

address: College Road

country: United Kingdom

institute: University of Nottingham

summary:
A microarray was developed to screen rodent samples for pathogens of zoonotic importance
In the work described here, a homologue to Yersinia pestis was found in rodent samples after screening with the microarray

sample_organism:
Mus musculus
Rattus norvegicus
Rattus rattus
Apodemus sylvaticus

platform_organism: Mycobacterium tuberculosis variant bovis

platform_organism: Mycobacterium avium subsp. paratuberculosis

platform_organism: Mycobacterium tuberculosis variant microti

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

platform_organism: Francisella tularensis subsp. tularensis

platform_organism: Francisella tularensis subsp. holarctica

platform_organism: Francisella tularensis subsp. mediasiatica

overall_design: A number of rodent samples from the UK and Canada were identified as carrying a homologue to a Yersinia pestis gene

first: Abu-Bakr

last: Abu-Median

first: Duncan

last: Hannant

first: Lisa

last: Yon

first: Paul

last: Barrow

first: Freddy

last: De Bree

first: Alex

last: Bossers


title: CGH analysis of allodiploid embryonic stem cells

status: Public on Jan 31 2016

city: Beijing

first: Xiaolong

last: Cui

address: No.1 Beichen West Road

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We performed array comparative genomic hybridization (aCGH) for our hybrid cells. All two analyzed hybrid ES cell liness were chromosomally stable.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Two hybrid ES cell lines were conducted to aCGH analyses. Two CGH array platforms were used.

first: Qi

last: Zhou


title: Genomic and transcriptomic study of allodiploid embryonic stem cells

type: Expression profiling by high throughput sequencing


title: DNA copy number variation analysis in hepatoma cell lines

status: Public on Feb 04 2016

city: Kanazawa

first: Kazunori

last: Kawaguchi

address: 13-1 Takara-Machi

department: Gastroenterology

country: Japan

institute: Kanazawa University

summary: We analyzed specific genes for DNA copy number variation in hepatoma cells and investigated whether these factors are related to liver cancer phenotype. Chromosome 20p, which includes the ligand for Notch pathways, Jagged1, was found to be amplified in several types of hepatoma cells. In conclusion, amplification of Jagged1 contributed to mRNA expression that activates the Jagged1-Notch signaling pathway in liver cancer and led to poor outcome.

overall_design: Comparative genomic hybridization arrays spotted with 1,440 bacterial artificial chromosome clones were used to assess copy number changes in 7 hepatoma cell lines and 2 non-hepatoma cell lines to identify chromosomal regions associated with the pathogenesis of liver cancer.

first: Masao

last: Honda

first: Taro

last: Yamashita

first: Shuichi

last: Kaneko


title: FissionNet

status: Public on Dec 31 2015

city: Ithaca

first: Jeffrey

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

summary:
Splicing profiling of deletion strains compared to wild-type control
1 replicate for each WT/deletion comparison

overall_design: Splicing sensitive S. pombe microarrays (Agilent-027365) were used to compare the splicing profile of various deletion strains relative to wild-type. The ΔSPAC1952.06c strain displayed reduced growth at 37°C so to elicit a strong phenotype we shifted this strain and the WT reference sample prior to collecting cells

first: Benjamin

last: Fair


title: Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models

status: Public on Dec 10 2015

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

summary: Understanding the structure and interplay of cellular signalling pathways is one of the great challenges in molecular biology. Boolean Networks can infer signalling networks from observations of protein activation. In situations where it is difficult to assess protein activation directly, Nested Effect Models are an alternative. They derive the network structure indirectly from downstream effects of pathway perturbations. To date, Nested Effect Models cannot resolve signalling details like the formation of signalling complexes or the activation of proteins by multiple alternative input signals. Here we introduce Boolean Nested Effect Models (B-NEM). B-NEMs combine the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks. We show that B-NEMs accurately reconstruct signal flows in simulated data. Using B-NEM we then resolve BCR signalling via PI3K and TAK1 kinases in BL2 lymphoma cell lines.

overall_design: 84 BL2 cell-line samples were hybridized to HGU133+2 Affymetrix GeneChips.

first: Alexandra

last: Schrader

first: Katharina

last: Meyer

first: Neele

last: Walther

first: Aline

last: Stolz

first: Maren

last: Schmidt

first: Elisabeth

last: Hand

first: Maurits

last: Evers

first: Katayoon

last: Shirneshan

first: Martina

last: Vockerodt

first: Wolfram

last: Klapper

first: Monika

last: Szczepanowski

last: Murray

first: Holger

last: Bastians

first: Lorenz

last: Trümper

first: Rainer

last: Spang

first: Dieter

last: Kube


title: Comparison of the expression profiles of R20291 strain and a R20291 strain after 4h, 6h, 8h, 14h, 38h of growth in vivo

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: Transcriptionnal profiling of C. difficile R20291 strain vs a R20291 strain after4h 6h 8h 14h 38h of growth in Vivo

overall_design: two-conditions experiments, WT strain after 4h, 6h, 8h, 14h, 38h, of growth in vivo, 4 biological replicates for each condition except 3 biological replicates for 14h, in an indirect design using a DNA preparation as Reference.

first: Amira

last: Barketi

first: Marc

last: Monot


title: CO2-neutral isoprene production using the cyanobacterium Synechocystis sp. PCC 6803

status: Public on Nov 13 2015

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

summary:
Cyanobacteria are phototrophic prokaryotes that can convert inorganic carbon as CO2 into organic carbon compounds at the expense of light energy. In addition, they need only a few inorganic nutrients and can be cultivated in high densities using non-arable land and seawater. This features qualified cyanobacteria as attractive organisms for the production of third generation biofuels as part of the development of future CO2-neutral energy production. Synechocystis sp. PCC 6803 represents one of the most widely used cyanobacterial model strains. On the basis of its available genome sequence and genetic tools, many strains of Synechocystis have been generated that produce different biotechnological products. Efficient isoprene production is an attractive goal, since this compound represents not only an energy-rich biofuel but is also used as chemical feedstock.
Here, we report on our attempts to generate isoprene-producing strains of Synechocystis. The cDNA of a codon-optimized plant isoprene synthase (IspS) was cloned under the control of different Synechocystis promoters, which ensure strong constitutive or light-regulated ispS expression. The expression of the ispS gene was quantified by qPCR, whereas the amount of isoprene was quantified using GC-MS. Incubation of our strains at different salt conditions had marked impact on the isoprene production rates. Under low salt conditions, a good correlation was found between ispS expression and isoprene production rate. However, the cultivation of isoprene production strains under salt-supplemented conditions decreased isoprene production despite the fact that ispS expression was salt-stimulated. The characterization of the metabolome of isoprene producing strains indicated that isoprene production might be limited by insufficient precursor levels.
Our isoprene production rates under low salt conditions were 2 - 6.5times higher compared to the previous report of Lindberg et al. (2010). These results can be used to guide future attempts establishing the isoprene production with cyanobacterial host systems.

overall_design: We monitored gene expression of an Synechocystis PCC6083 WT strain in comparison with the isoprene producing strain #642. Sample were done in biological replicates

first: Nadin

last: Pade

first: Sabrina

last: Erdmann

first: Heike

last: Enke

first: Frederik

last: Dethloff

first: Ulf

last: Dühring

first: Juliane

last: Wambutt

first: Joachim

last: Kopka

first: Wolfgang

last: Hess

first: Ralf

last: Zimmermann

first: Dan

last: Kramer

first: Martin

last: Hagemann


title: Expression data from retinoic acid injections into the third ventricle of F344 rats compared to vehicle injected rats

status: Public on Dec 01 2015

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

institute: Biomathematics & Statistics Scotland

summary:
Short day (8hrs of light/day) housed juvenile, male F344 rats were injected with 10^-5 M all-trans RA or vehicle (saline) into the third ventricle of the hypothalamus. 24 hours after RA injections rats were killed by decapitation after isoflurane inhalation at ZT3 and brains were dissected and frozen on dry ice. Hypothalamic arcuate nucleus tissue blocks were cut for RNA exaction.
4 rats per group were used giving 8 rats in total.

overall_design: Comparison of expression of genes were made between rats from RA injected vs vehicle injected groups.

first: Gisela

last: Helfer

middle: D

first: Peter

last: Morgan


title: Combined hepatic transcriptional effects of gamma radiation and depleted uranium on Atlantic salmon (Salmo salar)

status: Public on Oct 14 2015

city: Oslo

first: You

last: Song

address: Økernveien 94

department: Ecotoxicology and Risk Assessment

institute: Norwegian Institute for Water Research (NIVA)

summary: To study the short-term hepatic transcriptional changes and identify potential modes of action, Atlantic salmon (Salmo salar) were exposed to 70 mGy external gamma radiation, 0.25 mg/L depleted uranium and combination of these two. A combination of high density (60 k) custom oligonucleotide salmonid microarray and quantitative real-time reverse transcription polymerase chain reaction (qPCR) was used to perform gene expression analyses. Differentially expressed genes (DEGs) were determined using one-way analysis of variance (ANOVA) and Tukey posthoc tests. Functional enrichment analysis based on Gene Ontology (GO) was performed to link DEGs to their biological functions. The Salmo salar DEGs were further mapped to mammlian orthologs. By using ortholog DEGs, gene networks were built based on well-curated mammlian protein-protein interactions and pathways analyses were performed to link DEGs to specific toxicological/biological functions. The results obtained from microarray analysis were further verified using qPCR.

overall_design: Juvenile Atlantic salmon were exposed to external gamma radiation emitted from a cobalt-60 source for 5h and waterborne depleted uranium for 48 h. Liver were samples and used for gene expression analysis.

first: Brit

last: Salbu

first: Hans-Christian

last: Teien

first: Øystein

last: Evensen

first: Ole

last: Lind

first: Bjørn

middle: O

last: Rosseland

first: Knut

middle: E

last: Tollefsen


title: Differential gene expression in the duodenum, jejunum, and ileum among crossbred beef steers with divergent gain and feed intake phenotypes.

status: Public on Sep 19 2015

city: Clay Center

first: Amanda

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

summary:
Steer small intestine transcriptome
Evaluation of the naturally occurring transcriptome variation among beef steers with divergent gain and feed intake phenotypes.

overall_design: The transcriptome of three sections of the small intestine (duodenum, jejunum and ileum) were examined for expression differences that contribute to cattle feed efficiency.

last: Lindholm-Perry


title: miR-203 and miR-205 expression patterns identify subgroups of prognosis in cutaneous squamous cell carcinoma

status: Public on Aug 11 2015

city: Salamanca

first: Jesús

last: Pérez Losada

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary:
Identification of the expression pattern of miRNAs at different stages of skin cancer progression in a panel of murine skin cancer cell lines
miR-203 and miR-205 were differentially expressed in this panel, and were evaluated as biomarkers of prognosis in human cutaneous squamous cell carcinoma

sample_organism:
Mus musculus
Mus musculus x Mus spretus

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

overall_design: Three main tumor phenotypes: (i) Squamous non-malignant: Five non-malignant cell lines: three of them immortalized keratinocyte cell lines, and of them two papilloma cell lines. (ii) Three malignant squamous cell lines. (iii) Five malignant spindle cell lines. One replicate per array, except A5 that was done in duplicate as control

first: Javier

last: Cañueto

first: Ester

last: Cardeñoso-Álvarez

first: Juan

last: García-Sánchez

first: Purificación

last: Galindo-Villardón

last: Vicente-Galindo

first: Diego

last: Alonso-López

last: de las Rivas

first: José

last: Valero

first: Estefanía

last: Moyano-Sáez

first: Emilia

last: Fernández-López

first: Jian

last: Mao

first: Andrés

last: Castellanos-Martín

first: Concepción

last: Román-Curto

last: Pérez-Losada


title: Whole blood transcriptome analysis of Mycoplasma mycoides subsp, mycoides-infected cattle confirms immunosuppression but does not reflect local inflammation

status: Public on Jun 20 2015

city: Montpellier

first: Rodrigues

last: Valérie

address: TA A30/G

department: BIOS

institute: CIRAD

summary: In order to assess the use of whole blood transcriptome analysis to study cattle-Mmm interactions, we performed this study on 6 cattle, comparing the blood transcriptome before infection with the beginning of the clinical signs. Statistical analysis enabled Mmm-infected animals to be clearly distinguished from healthy ones. Functionnal analysis revealed that 680 genes were differentially expressed, confirming previous results as immunosuppression. Surprisingly, whoole blood transcriptome analysis didn't reflect inflammation, a highly characteristic local sign of these disease. This absence on inflammation signs results were confirmed by RT-qPCR.

overall_design: Whole blood gene expression was measured for each of 6 animals before infection and at the beginning of the clinical signs of CBPP. A paired sample statistical analysis was performed to identify diferentially expressed genes between healthy and infected status.

first: Valérie

last: Rodrigues

first: Philippe

last: Holzmuller

first: Carinne

last: Puech

first: Hezron

last: Wesonga

first: François

last: Thiaucourt

first: Lucia

last: Manso-Silvan


title: The Mot1 ATPase and Spt16 Histone Chaperone Cooperatively Regulate Transcription

status: Public on May 16 2016

city: Charlottesville

first: David

last: Auble

state: VA

address: Box 800733 Jordan Hall University of Virginia Health System

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: Mot1 is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis, and in so doing exerts global effects on transcription.  Spt16 is also essential and functions globally in transcriptional regulation as a component of the FACT histone chaperone complex.  Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae.  As expected, Mot1 was found to control TBP levels at co-regulated promoters.  In contrast, Spt16 did not affect TBP recruitment.  Interestingly, Mot1 was required for Spt16 recruitment to co-activated promoters.  In contrast, Spt16 levels in gene coding regions were unaffected by Mot1 as well as RNA polymerase II density.  The co-localization of Mot1 and Spt16 at promoters and the broad overlap in the sets of genes they control is consistent with physical and genetic interactions between them.  The data support a model in which these factors participate in a regulatory pathway in which Mot1 acts upstream of Spt16.

overall_design:
Tiling arrays covering the entirety of the S.cerevisiae genome were used to identify the effects of Mot1 and Spt16 on RNA expression genome-wide.  All samples were done in biological duplicates.  The average signal from the spt16-197 samples was compared to the SPT16-WT to determine changes in expression.  The average signal from the double mutant mot1-42 spt16-197 was compared to both SPT16-WT and MOT1-WT.  The MOT1-WT data was previously published by our lab and is available at GEO accession GSM456548.  Comparisons were made from our Spt16 dataset to the previously published MOT1-WT and mot1-42 data, and the entire study is available at GEO accession GSE18283.
Differential RNA (spt16-197/SPT16): spt16-197_over_SPT16-WT.bar
Differential RNA (mot1-42 spt16-197/SPT16): dbl_mut_over_SPT16-WT.bar
Differential RNA (mot1-42 spt16-197/MOT1): dbl_mut_over_MOT1-WT.bar

first: Jason

last: True

first: Joseph

middle: J

last: Muldoon

first: Melissa

middle: N

last: Carver

first: Kunal

last: Poorey

first: Stefan

last: Bekiranov

middle: T


title: Multi-platform Characterization of Stage I Lung Adenocarcinoma (miRNA profiling)

status: Public on Apr 30 2015

city: Bethesda

first: Ana

middle: I

last: Robles

state: MD

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

summary: microRNA expression profiling of Stage I Lung Adenocarcinoma and non-tumor adjacent tissues. The Nanostring nCounter Human miRNA Expression Assay Kit version 1.6 (Nanostring, Seattle, WA) was used to obtain microRNA profiles of tumor and adjacent non-tumor tissues excised from Stage I Lung Adenocarcinoma patients.

overall_design: Total cellular RNA was extracted from tumor and matching adjacent non-tumor lung using miRNA Kit (QIAGEN), according to the manufacturer’s instructions, and 100 ng were used for hybridization to Nanostring nCounter Human miRNA Expression Assay Kit version 1.6 (Nanostring, Seattle, WA) following processing protocol recommended by the manufacturer.

first: Curtis

last: Harris


title: Choline transporter-like1 is required for plasmodesmal targeting of Potato leafroll virus movement protein MP17 and long-distance assimilate transport

status: Public on Jun 01 2016

city: Erlangen

first: Uwe

last: Sonnewald

address: Staudtstr. 5

department: Biology, Biochemistry

institute: Friedrich-Alexander-University

summary: Macromolecular trafficking and cell-to-cell communication in plants occurs via plasmodesmata (PD). Currently, little is known about the proteins defining these sophisticated cell-to-cell contacts. To uncover proteins required for PD structure and function we made use of the 17 kDa movement protein (MP17) of the Potato leafroll virus (PLRV). The protein is required for cell-to-cell movement of the virus and localizes specifically to branched PD in source tissues. By forward genetic screening for Arabidopsis mutants with altered PD binding of MP17, several mutants were found. Map-based cloning of one of these mutants revealed a mutation in the choline transporter-like 1 (CHER1) protein. The mutation abolished plasma membrane localization of the protein. As consequence phosphatidylcholine levels and PD binding of MP17 decreased. Transcriptome analysis revealed a down-regulation of defense genes and genes involved in the synthesis of very long chain fatty acids, indicating an impairment of lipid signaling. Furthermore, cher1 mutants showed a reduced assimilate export and stunted growth. These findings highlight the emerging role of phospholipids, especially in the context of PD structure and function as well as potential binding sites for plasma membrane- and PD-associated proteins, which has been neglected for a long time.

overall_design: light exposed source leaves from wild type Col-0, T-DNA insertion line cher1-4 and mutant cher1-5 (10 weeks old). Samples: per pool  2 source leaves from 4 different plants, taken in the afternoon; wildtype (WT): Col-0, cher1-4: T-DNA insertion line SALK-065853 (ecotype Col-0, kanamycin resistance), cher1-5: Col-0 with GGA -->GAA at position 740 of cds

first: Katrin

last: Link

first: Stephen

last: Reid


title: Multi-platform Characterization of Stage I Lung Adenocarcinoma (Genome-wide DNA Methylation)

summary: Genome wide DNA methylation profiling of Stage I Lung Adenocarcinoma and non-tumor adjacent tissues. The Illumina Infinium 27k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included tumor and adjacent non-tumor tissues excised from a cohort of 35 patients with Stage I Lung Adenocarcinoma. Candidate prognostic biomarkers were validated by pyrosequencing in independent cohorts.

overall_design: Total genomic DNA was bisulfite converted and hybridized to Infinium Human Methylation27Beadchips. Fluorescent signals were collated via Bead Studio software and converted into β-values. Illumina Bead Studio software output data were normalized using SSN (simple scaling normalization), to correct for dye bias and transformed into M-values (M = log2 intensity of methylated probe/ intensity of unmethylated probe), using the R package lumi.


status: Public on Sep 01 2015

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

summary:
Pancreatic Gene Expression from Wild-Type, Stat1-Transgenic, and Stat1-CC-Transgenic Mice. This data was part of the set of data utilized to identify PARP9/DTX3L as a novel antiviral gene.
Keywords: transgene state analysis

overall_design: RNA was extracted from the pancreas of 3 mice per genotype (wild-type, Stat1-Transgenic, Stat1-CC-Transgenic). Comparisons were made between Stat1-Transgenic and Stat1-CC-Transgenic mice.

first: Yong

last: Zhang

first: Dailing

last: Mao

first: Dhara

middle: A

first: William

last: Roswit

first: Guangming

last: Huang

first: Ronald

last: McCarthy

first: Jeffrey

last: Atkinson

first: Eugene

last: Agapov

first: Nadezhda

last: Yun

first: Slobodan

last: Paessler

first: T

last: Lawson

first: Natalie

last: Omattage

first: Tom

last: Brett

first: Michael

last: Holtzman


title: MicroRNA signature in skeletal muscle in type 2 Diabetes [human]

status: Public on Apr 25 2015

city: Melbourne

first: Celine

last: Latouche

state: VIC

address: 75 Commercial Road

country: Australia

institute: Baker IDI Heart and Diabetes Institute

summary: The current study aimed to address the hypothesis that programmed expression of key miRNAs in skeletal muscle mediates the development of insulin resistance, and consequently long-term health. We thus examined microRNA signatures in skeletal muscle of unmedicated newly diagnosed human pre-diabetics and type 2 diabetics.

overall_design:
Skeletal muscle biopsies were obtained from the vastus lateralis from males with pre-diabetes (PD, n=5) or type 2 diabetes mellitus (T2DM, n=6) along with age and sex-matched healthy volunteers (H, n=5).
Ramaciotti Centre for Genomics (UNSW, sydney, Australia)


title: MicroRNA signature in skeletal muscle in insulin resistant rats

summary: The current study aimed to address the hypothesis that programmed expression of key miRNAs in skeletal muscle mediates the development of insulin resistance, and consequently long-term health. We thus examined microRNA signatures in skeletal muscle of programmed insulin resistant rats offspring from high fat-fed dams vs control offspring from chow fed dams.

overall_design:
Skeletal muscle (soleus) was collected from the hind limb of 1 year old male offspring (6 from control dams, 6 from high fat-fed dams) .
Ramaciotti Centre for Genomics (UNSW, sydney, Australia)


title: Combined effects of ZnO and TiO2 nanoparticles on functional gene expression of Nitrosomonas europaea

status: Public on Jun 23 2015

city: Nanjing

first: Junkang

last: Wu

state: Jiangsu

address: 2 Sipailou Street

department: Energy and environment

institute: Southeast University

summary: To further explore and differentiate the biotoxicity mechanisms of individual nanoparticles (NPs) and NP mixture on Nitrosomonas europaea (N. europaea, ATCC 19718) at genetic level, a genome-sequenced model ammonia oxidizing bacterium (AOB) commonly detected in the activated sludge of biological wastewater treatment plants, the induced whole-genome expressions were analyzed with the high throughput Microarray technique, after the dose-dependent changes of N. europaea’s physiological, metabolic and AMO enzyme activities in single and dual component NP systems was evaluated.

overall_design: NP stress induced gene expressions were measured after 6hr exposure to 10 ppm nano-ZnO, 50 nano-TiO2 and their mixture.Three independent experiments were performed  for each experiment.

first: Ran

last: Yu


title: R. sphaeroides pRCcsR1-4 vs. R. sphaeroides 2.4.1 pRK415 (aerobic conditions)

status: Public on Mar 23 2015

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

summary: Transcriptional profiling of R. sphaeroides pRCcsR1-4 comparing to control R. sphaeroides 2.4.1 pRK415 under aerobic conditions

overall_design: Two strain experiment under aerobic conditions. 6 Biological replicas, independetly grown and harvested at OD660=0,4; 1-3 pooled in replicate 1, 4-6 pooled in replicate 2

first: Bork

last: Berghoff

first: Fabian

last: Billenkamp


title: MicroRNA signature in skeletal muscle in type 2 Diabetes and insulin resistant rats

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

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series


title: SW1 mutant vs Shewanella piezotolerans WP3 wild-type strain

status: Public on Mar 04 2015

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: The prophage and RF DNA of SW1 were removed from WP3 to construct the phage-free strain. The two strains were cultured at 20MPa and 4°C and the transcriptional profiles were compared.

overall_design: Three biological replicates sample and 6 technical replicates for each experiment

first: Fengping

last: Wang


title: hns mutant vs Shewanella piezotolerans WP3 wild-type strain 20C

status: Public on Jul 01 2014

summary: The hns gene was deleted from WP3 genome to construct the WP3Δhns strain. The two strains were cultured at 20°C and the transcriptional profiles were compared.


title: hns mutant vs Shewanella piezotolerans WP3 wild-type strain 4C

summary: The hns gene was deleted from WP3 genome to construct the WP3Δhns strain. The two strains were cultured at 4°C and the transcriptional profiles were compared.


title: lexA mutant vs Shewanella piezotolerans WP3 wild-type strain

status: Public on Mar 13 2015

summary: The lexA gene was deleted from WP3 genome to construct the WP3ΔlexA strain. The two strains were cultured at 20MPa and 4°C and the transcriptional profiles were compared.


title: SW1 mutant vs. Shewanella piezotolerans WP3 wild-type strain

status: Public on Jan 30 2013

summary: The prophage and RF DNA of SW1 were removed from WP3 to construct the phage-free strain. The two strains were cultured at 4°C and the transcriptional profiles were compared.

overall_design: WP3ΔSW1 is the test sample and WP3 wild-type is the reference sample. Three independent cultures were used for RNA extraction, and the RNA samples were combined into one sample for microarray. Each microarray slide has 3 spots for a single gene, and as dye-swaps were performed, 6 spots were used to determine the expression level of one gene.


title: hns mutant vs Shewanella piezotolerans WP3 wild-type strain 4C and 20C


title: Cellular mechanisms of salt adaptation. Nicotiana tabacum BY-2 cell cultures as model

status: Public on Nov 28 2012

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary: Cell adaptation to high salinity levels implicates the modification of different cellular, physiological and molecular mechanisms. However, studies about the cellular mechanisms that are implicated in salt adaptation are scarce in the literature. Tobacco BY-2 cell cultures are very homogeneous and are characterized by a continuous cell grow and high proliferation rate. These features make these cells a good model system. For this study, we have obtained a stable tobacco cell line adapted to grow at 250 mM of NaCl. To obtain a general view of this process, we have followed a microarray technique. Gene expression was analyzed using the Affymetrix microarray technique. We have used a microarray designed by Edwards et al. (2010) in tobacco (Total probes: 43768).

overall_design: Comparison between a control cell line of tobacco BY-2 cells and a salt adapted cell line to 250 mM of NaCl. The cell cultures have been been grown in LS medium and in darkness at 26C. 100 mg of fresh tobacco cell growing at exponential phase was grinded thoroughly in liquid nitrogen with a mortar and pestle. Total RNA was extracted with the RNeasy Plant Mini Kit from Qiagen according to the supplier's instruction. These were then hybridized to Affymetrix chips.

first: Enrique

last: Olmos


title: R. sphaeroides pRKPcrZ vs. R. sphaeroides pRK4352 under low oxygen conditions

status: Public on Aug 15 2012

summary: Transcriptional profiling of R. sphaeroides pRKPcrZ compared to control R. sphaeroides pRK4352 under low oxygen conditions. In this study we compared the transcriptome of a PcrZ over-expression strain to a control strain. PcrZ is the first small non-coding RNA, which is involved in the complex regulatory network of photosynthesis gene regulation in Rhodobacter sphaeroides. It counteracts the formation of photosynthetic complexes in a redox dependent manner.

overall_design: Two-strain experiment at low oxygen conditions (0.5 mg/L O2)

first: Nils

last: Mank


title: Rhodobacter sphaeroides WT 2.4.1 under singlet oxygen stress

status: Public on Nov 14 2012

summary: Transcriptional and translational profiling of R. sphaeroides WT 2.4.1 under singlet oxygen stress compared to control (no stress) conditions

overall_design: RNA samples collected at time-point zero and at different time-points after singlet oxygen stress were analyzed by two-color microarrays


title: miRNA expression differences in tumor and benign prostate tissues

status: Public on Dec 08 2014

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

summary: We investigated the global miRNA expression in prostate tumor and benign tissues by qPCR expression profiling.

overall_design: qPCR gene expression profiling.  miRNA expression was measured in prostate benign and tumor tissues from cancer patients by using miRNA Taqman plates.

first: Holger

last: Sueltmann

first: Marc

last: Johannes

first: Jan

last: Brase


title: Gene expression profiles in individuals with asymptomatic infections against cognate household members with dengue fever

status: Public on Sep 06 2013

city: Kuala Lumpur

first: Shamala

middle: Devi

last: Sekaran

address: Faculty of Medicine, University of Malaya

department: Department of Medical Microbiology

country: Malaysia

institute: University of Malaya

summary: Dengue represents one of the most serious life-threatening vector-borne infectious diseases that afflict ~50 million people across the globe annually. Whilst symptomatic infections are frequently reported, asymptomatic dengue largely remain unnoticed. The immune correlates conferring protection to individuals that remain clinically asymptomatic have seldom been investigated. We determined the gene expression profiles of host immune factors in individuals with asymptomatic infections, and whose cognate household members showed symptoms and signs consistent to clinical dengue infection. Results provide insight in association of certain host genes to protection against clinical dengue.

overall_design: Blood samples were collected from Dengue Fever (DF) and Dengue Haemorrhagic Fever (DHF) patients in Malaysia who were admitted to university of Malaya Medical Centre (UMMC), Ampang Hospital (AmpangHospital), and Hospital Tengku Ampuan Rahimah (HTAR) Klang. Blood from their asymptomatic household members were also collected. Their peripheral blood mononuclear cells (PBMCs) were isolated. 29 sample pairs (SP) of dengue patients and their accompanying asymptomatic household members were chosen on the following basis for two-channel microarray experiments: patients who have shown positive results for DENV infection with at least 2 diagnostics tests indicating positivity. Positive results for the IgM-captured ELISA were P/N ratio more than 2.0, while total antibody titer of more than 1:2560 or 4 fold increase from acute to convalescence phase was considered positive in HI assay. PRNT, a neutralization test, was used as a measure for levels of neutralizing antibodies and was considered high when it was more than 1:640, based on a reduction neutralization of 50%.

first: Adeline

middle: S

last: Yeo

first: Nur

last: Azhar

first: Wanyi

last: Yeow

first: Mohammad

last: Khan

first: Shankar

last: Muthu

first: Anusyah

last: Rathakrishnan

first: Azliyati

last: Azizan

first: SM

first: Rishya

last: Manikam


title: Gene expression profiles of gliomas in formalin-fixed paraffin-embedded material

status: Public on Jul 01 2012

city: Rotterdam

first: Lonneke

middle: AM

last: Gravendeel

state: South Holland

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

summary: In this study we have performed expression analysis using paired FF-FFPE glioma samples. We show that expression data from FFPE glioma material is concordant with expression data from matched FF tissue, and can be used for molecular profiling in gliomas.

overall_design:
In this study we have performed expression analysis using 55 paired FF-FFPE glioma samples (HU133 plus 2.0 arrays (FF) and Human Exon 1.0 ST arrays (FFPE)). The most informative probe sets were selected based on variance
This Series contains the FFPE data only.  FF data set was previously submitted (GSE16011).

first: Johan

last: de Rooi

first: Paul

middle: H

last: Eilers

first: Martin

last: van den Bent

first: Peter

last: Sillevis Smitt

first: Pim

last: French


title: Pam3Cys-treated HUVEC before and after TLR2 knockdown

status: Public on Jun 23 2011

city: San Francisco

first: Kevin

last: Wilhelmsen

state: CA

address: 513 Parnassus Ave.

department: Anesthesia

country: USA

institute: University of California, San Francisco

summary: The vascular endothelium is integrally involved in the host response to infection and in organ failure during acute inflammatory disorders such as sepsis. Gram-negative and gram-positive bacterial lipoproteins circulate in sepsis and can directly activate the endothelium by binding to endothelial cell (EC) Toll-like receptor 2 (TLR2). In this report, we perform the most comprehensive analysis to date of the immune-related genes regulated after activation of endothelial TLR2 by bacterial di- and triacylated lipopeptides. We found that TLR2 activation specifically induces the expression of IL6, IL8, CSF2, CSF3, ICAM1 and SELE by human umbilical vein ECs and human lung microvascular ECs. These proteins participate in neutrophil recruitment, adherence and activation at sites of inflammation. Significantly, our studies demonstrate that bacterial lipopeptides activate human EC exclusively through TLR2, that TLR2-mediated EC responses are specifically geared towards recruitment, activation, and survival of neutrophils and not mononuclear leukocytes, and that ECs do not require priming by other inflammatory stimuli to respond to bacterial lipopeptides. This study suggests that endothelial TLR2 may be an important regulator of neutrophil trafficking to sites of infection in general, and that direct activation of lung endothelial TLR2 may contribute to acute lung injury during sepsis.

overall_design: qPCR gene expression profiling.  HUVEC monolayers were left untreated or treated with 10 μg/mL of Pam3Cys for 3 hr prior to lysis. RQ values were calculated using the 2-ΔΔCt method. Three biological replicates and one technical replicate were analyzed in both the untreated and Pam3Cys-treated TLR2 transfected groups. Four biological replicates and one technical replicate were analyzed in the Pam3Cys-treated group (the data for three untransfected samples and one control siRNA-transfected sample were combined).

first: Kailin

last: Mesa

first: Arun

last: Prakash

first: Fengyun

last: Xu

first: Judith

last: Hellman