title: Detailed analysis of 6p and 1q amplifications in urothelial carcinoma reveals SOX4 as an auxiliary target on 6p, and BCL9, CHDL1, MCL1, SETDB1, and HIF1B as putative targets on 1q.

city: Lund

first: Mattias

last: Aine

address: Klinikgatan 28

department: Oncology

institute: Lund University

summary:
Background: Previous array CGH analyses have revealed several recurring genomic alterations in urothelial carcinoma. The most common genomic amplifications occur at 6p22 and 1q21-24. The main target gene at 6p22 is believed to be E2F3. This gene is frequently co-amplified with CDKAL1 and SOX4 and there are reports on 6p22 amplifications that do not include the E2F3 locus. Previous array CGH analyses have indicated multiple possible target regions at 1q21-24. However, due to complex rearrangements it has been difficult to identify specific 1q21-24 target regions and target genes.

Results: We show that the most commonly amplified gene at 6p22 is SOX4 and that SOX4 can be amplified and over expressed without E2F3 or CDKAL1 being included in the amplicon. Hence, our data point to SOX4 as an auxiliary amplification target at 6p22. We further show that at least three amplified regions are observed at 1q21-24. Copy number data, combined with gene expression data, highlighted BCL9 and CHD1L as possible targets in the most proximal region and MCL1, SETDB1, and HIF1B as targets in the middle region, whereas no obvious gene targets could be determined in the most distal amplicon. We also highlight the enrichment of G4 quadruplex sequence motifs and the high number of intraregional sequence duplications, both known to contribute to genomic instability, as prominent features of the 1q21-24 region.

Conclusions: Our detailed analyses of the 6p22 amplicon in urothelial carcinomas suggest SOX4 as an auxiliary target gene for amplification. We further demonstrate three separate target regions for amplification at 1q21-24 and identified BCL9, CHD1L, MCL1, SETDB1, and HIF1B as likely target genes within these regions.

overall_design:
The study was conducted on genomic DNA from 68 primary fresh-frozen urothelial carcinoma tumors analysed using a Agilent SurePrint G3 4x180k Custom CGH Microarray Platform (028432). Samples were selected based on the presence of copy number alterations observed on lower resolution genomic data (32K BAC array).

The majority of the BAC data is publicly available in GEO submissions GSE32535 and GSE19915. CN profiles for a minority of samples were derived from Illumina Methylation27k arrays according to Lauss et al 2012 [PMID: 22705924] and can be recreated from the data deposited in GSE33510 (derived CN data). Sample names are the same between all studies.

This dataset also partly overlaps with Series GSE32894 (gene expression data). Names of the overlapping sample names are the same and indicated in the description field.  Data from GSE32894 was used to calculate correlations between CN and gene expression.

first: Pontus

last: Eriksson

first: David

last: Lindgren

first: Gottfrid

last: Sjödahl

last: Höglund


title: S. cerevisiae L3262: Control vs. SPT15 multiple point mutant strains, Ets2 and Ets3

status: Public on Sep 01 2013

city: Seoul

first: Hye Yun

last: Moon

state: Seoul

address: , 221 Heukseok-dong, Dongjak-gu

department: Department of Life Science

country: South Korea

institute: Chung-Ang university

summary: Transcriptional profiling of ethanol tolerant strains Ets2 and Ets3 comparing control Saccharomyces cerevisiae L3262 with ethanol tolerant strains Ets2 and Ets3, through screening a mutant library of SPT15 of Saccharomyces cerevisiae L3262.

overall_design: Four-condition experiment, L3262 vs. Ets2 or Ets3 strains. Biological replicates: 4 control, each 2 transfected(Ets2, Ets3), independently grown and harvested. One replicate per array.

first: Hyeyun

first: Hyunah

last: Kang


title: Chromatin function of IkBa: ChIP-on-chip of IkBa

status: Public on Aug 28 2013

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

type: Genome binding/occupancy profiling by genome tiling array

summary:
The Inhibitor of the NFkB, IkBa, is the main regulator of the NFkB pathway. Our data has demonstrated that there is an alternative function for IkBa in the chromatin that affects HOX and other developmental genes.

Keywords: CHIP-chip

overall_design: Chip-on-chip analysis has demonstrated that IkBa associates to the promoters of several genes. Chromatin fragments were obtained from NIH-3T3 cells and precipitated with 3 different IkBa comercial antibodies (raised in mouse, goat and rabbit), and fold enrichment was compared to input.

first: Anna

last: Bigas

first: Lluis

last: Espinosa


title: Transcriptome microarray of wildtype, relA, expI and rpoS Pectobacterium atrosepticum strains in PMB media

status: Public on Aug 30 2013

city: Cambridge

first: Steven

middle: Douglas

last: Bowden

address: Building O, Downing Site

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

summary:
Whole genome analysis of gene expression by Pectobacterium atrosepticum strain SCRI1043 wildtype and its relA, expI and rpoS deletion mutants when grown to exponential and stationary phase in PMB media.
The data is further described in Bowden et al (2013) Virulence in Pectobacterium atrosepticum is regulated by a coincidence circuit involving quorum sensing and the stress alarmone, (p)ppGpp. Molecular Microbiology. DOI: 10.1111/mmi.12369

overall_design: A 24 chip study using total RNA recovered from three separate wild-type cultures of Pectobacterium atrosepticum SCRI1043 and three separate cultures from three single mutant strains of SCRI1043 possessing deletions within relA (ECA3569), expI (ECA0105) or rpoS (ECA3530) when grown in Pel Minimal Broth (PMB) media to log-phase (6h) or early stationary phase (14h) growth. Each chip measures the expression level of 4,472 genes from Pectobacterium atrosepticum SCRI1043 with eight 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

middle: D

first: Martin

last: Welch


title: Profiling of miRNA expression in mouse SHAM kidneys

status: Public on Aug 31 2013

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

overall_design: 9–12 weeks old male C57BL/6 mice were purchased from Charles River. Mice underwent anesthesia by intraperitoneal injection of pentobarbital (50 mg/kg body weight) and were subjected to Unilateral Ureteral Obstruction (UUO). After standard laparotomy, the left proximal ureter was exposed and ligated with 4-0 silk at two points. The sham operation consisted of a similar identification of the left ureter without ligation.  Treated (S numbers) and non-treated (C numbers) mice miRNA expressions were then compared.

first: Michael

last: Perrais


title: Transcriptional analysis of the response of Caldicellulosiruptor saccharolyticus to different H2 partial pressures

city: Raleigh

first: Robert

middle: M

last: Kelly

state: MI

address: Campus Box 7905

department: Chemical and Biomolecular Engineering

country: USA

institute: North Carolina State University

summary: Caldicellulosiruptor saccharolyticus is an extremely thermophilic, gram-positive anaerobe which ferments a broad range of substrates to mainly acetate, CO2, and hydrogen gas (H2). Its high hydrogen-producing capacity make this bacterium an attractive candidate for microbial biohydrogen production. However, increased H2 levels tend to inhibit hydrogen formation and leads to the formation of other reduced end products like lactate and ethanol.   To investigate the organism’s strategy for dealing with elevated H2 levels and to identify alternative pathways involved in the disposal of the reducing equivalents, the effect of the hydrogen partial pressure (PH2) on fermentation performance was studied. For this purpose cultures were grown under high and low PH2 in a glucose limited chemostat setup.   Transcriptome analysis revealed the up-regulation of genes involved in the disposal of reducing equivalents under high PH2, like lactate dehydrogenase and alcohol dehydrogenase as well as the NADH-dependent and ferredoxin-dependent hydrogenases. These findings were in line with the observed shift in fermentation profiles from acetate production under low PH2 to a mixed production of acetate, lactate and ethanol under high PH2. In addition, differential transcription was observed for genes involved in carbon metabolism, fatty acid biosynthesis and several transport systems. The presented transcription data provides experimental evidence for the involvement of the redox sensing Rex protein in gene regulation under high PH2 cultivation conditions.   Overall, these findings indicate that the PH2 dependent changes in the fermentation pattern of C. saccharolyticus are, in addition to the known regulation at the enzyme/metabolite level, also regulated at the transcription level.

overall_design: Two conditions: low H2 partial pressure and high H2 partial pressure, both at steady state growth were harvested for a dye-flip microarray experimental design. Biological replicates were harvested for both conditions and combined prior to cDNA synthesis. Both conditions were labeled with cy3 and cy5 dyes allowing for a technical replicate of hybridization in addition to the biological replicates.

first: Abraham

middle: A

last: Bielen

first: Marcel

middle: R

last: Verhaart

first: Amy

middle: L

last: VanFossen

first: Sara

middle: E

last: Blumer-Schuette

first: Alfons

middle: J

last: Stams

first: John

last: van der Oost

first: Servé

last: Kengen


title: Unilateral once daily milking locally induces differential gene expression in both mammary tissue and milk epithelial cells revealing mammary remodeling

status: Public on Aug 27 2013

city: JOUY-EN-JOSAS

first: Laurent

last: GALIO

address: Domaine de Vilvert

institute: INRA

summary: Once daily milking reduces milk yield and alters mammary transcriptome resulting in a decrease in milk protein synthesis as well as an induction of the apoptotic signaling networks. A local regulation due to milk stasis in the tissue could contribute to this effect but such mechanisms have not yet been described. To challenge this hypothesis, cows were milked unilaterally, once daily on one udder half and twice daily on the other one, and variations in gene expression were studied in biopsies as well as in mammary epithelial cells (MEC) shed into milk during the lactation process (milk MEC). This study therefore also contributes to decipher if transcript variations in milk purified MEC can reflect that of the mammary tissue.  We compared the mammary transcript profiles in biopsies collected from unilaterally once versus twice-daily milked udder halves, 504 transcripts were differentially expressed: 193 and 232 transcripts were up- and down-regulated, respectively.   A first category of transcripts, which accumulation levels are mostly up-regulated, relates to mechanisms involved in cell renewal, such as cell cycle, cellular growth and proliferation, cell death and cellular development. A second family, mostly down-regulated, is involved in small molecule biochemistry, amino acid, lipid and carbohydrate metabolisms as well as molecular transport. A third category, mostly up-regulated, includes transcripts expressed in non-epithelial mammary cells such as adipocytes, endothelial and immune cells and cells from the connective tissue.   These results are consistent with previous data showing a decrease in mammary synthesis activity and an activation of cell death during once daily milking. They further suggest that during once daily milking the local milk accumulation has a major effect on mammary remodeling. Interestingly, some transcripts belonged to a third family described as « molecular transports ».   The expression of the 21 mRNA was then analyzed by RT-par in MEC (Table 4). Seven transcripts (NUCB2, RNASE4, ABCG2, RNASE1, SLC34A2, Cap1, FABP3, LALBA, SCD) were significantly down-regulated in milk purified MEC. Six were also significantly down-regulated in mammary biopsies. These transcripts are mostly involved in milk synthesis.  We therefore conclude that milk purified MEC cannot be used as general markers of variations occurring in the mammary tissue but that variations in some transcripts listed above can be useful indicators.

overall_design: In this experimental design, udder halves were unilaterally milked once daily and the contralateral udder halves twice daily. Each mammary biopsy RNA sample from one udder half was compared to the one of the contralateral udder half in 5 dye-swaps corresponding to 5 animal replications, minimizing the animal variability. One dye swap corresponded to one comparison meaning two slides.

first: Marion

last: Boutinaud

last: Galio

first: Laurence

last: Finot

first: Vanessa

last: Lollivier

first: Sandra

last: Wiart

first: Diane

last: Esquerre

first: Eve

last: Devinoy


title: Effect of cFP on gene expression in Vibiro cholerae

status: Public on Aug 13 2013

city: Pittsburgh

first: James

last: Bina

state: PA

address: 450 Technology Dr

department: Microbiology and Molecular Genetics

institute: University of Pittsburgh

summary: Vibrio cholerae is a Gram negative, motile, facultative anaerobic bacterium, and the causative agent of cholera, a severe diarrhoeal disease, which untreated can rapidly lead to dehydration, hypotensive shock, and death. Cholera is a significant human disease that is estimated to affect 3-5 million people each year. The mechanism by which V. cholerae regulates virulence gene expression in vivo is unknown, but a number of studies have suggested that low molecular weight signally molecules may be important in modulating gene expression. cFP is a low molecular weight cyclic dipeptide produced by multiple Vibrio species. Evidence previously generated in our laboratory showed that cFP inhibited the production of the virulence factors cholera toxin (CT) and the toxin coregulated pilus (TCP) in O1 El Tor V. cholerae strain N16961 during growth under virulence gene inducing conditions. cFP inhibition of CT and TCP production correlated with reduced transcription of several regulators that belong  to the ToxR regulon. To identify additional cFP-responsive genes we performed microarray experiments with the O1 El Tor V. cholerae strain N16961. In these experiments N16961 was grown under virulence gene inducing conditions in the presence and absence of cFP before RNA was extracted and hybridized to microarrays. The results showed that cFP positively affected the expression of the LysR-family regulatory protein LeuO. This finding suggests the possibility that LeuO may be mediating cFP-dependent regulation of gene expression in response to environmental cFP.

sample_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: V. cholerae N16961 was grown under AKI growth condition in the presence or absence of 1 mM cFP for 2.5 or 3 hours when total RNA was extracted, differentially labelled and hybridized to microarrays. Four independent experiments were performed.

first: Jim

first: Xiaowen


title: Gene expression during testis development in Duroc boars

city: Aarhus

first: Lene

middle: Nagstrup

last: Conley

state: Denmark

address: Langelandsgade 140

department: Department of Chemistry

country: Denmark

institute: University of Aarhus

summary: The aim of the study was to combine understanding between a timeline for molecular and macroscopic functions in the testis of the Duroc boar.  To achieve this, cluster and pathway analysis was performed based on microarray transcripts from four pubertal timepoints with known steroidogenic status and known morphological maturation status.

overall_design: Gene expression study of testes biopsies from Duroc boars, taken at age 12, 16, 20 and 27 weeks of age, using in-house printed porcine two-colour cDNA microarrays.

first: Siri

last: Lervik

first: Anja

last: Kristoffersen

first: Ingrid

last: Olsaker

middle: N

first: Irma

last: Oskam

first: Jakob

last: Hedegaard

first: Erik

last: Ropstad


title: Host and pathogen interaction: time course [C. albicans]

status: Public on Aug 26 2013

city: Hsin-chu

first: Yan-Yu

last: Chen

address: No. 101, Section 2, Kuang-Fu Road

department: Chemical Engineering

country: Taiwan

institute: NTHU

summary: The interaction between fungal pathogen and host during infection is a complex and dynamic process. To resolve this, we chose the zebrafish model organism as the host to study C. albicans infection via systems biology approach. Transcriptome microarray data and histological analysis of surviving fish were sampled at different post-infection time points. The dynamic variations of significant genes expression profiles in C. albicans and zebrafish were concurrently analyzed by principal component analysis (PCA). The PCA results clearly indicated that the infection of C. albicans can be divided into three phases that include adhesion, invasion and damage phases. The results were highly consistent with subsequent histological analysis. Furthermore, we found the primary ontology function of genes with significant variations in both C. albicans and zebrafish is iron related. Most of the iron related genes in C. albicans were over-expressed in late stage, while most of the iron related genes in zebrafish were suppressed at the same phase of infection. It suggested that the iron homeostasis function of the host was shut-down when massive hemorrhage in zebrafish occurred during later stages of infection. At the same time, the iron scavenging function of C. albicans was activated. This implied the competition for iron is an important issue between the host and the fungal pathogen during infection. When we administered excess iron into the microenvironment of infection site, the infection process was significantly delayed. That indicated the virulence of C. albicans is correlated with its protein-bond iron scavenging strategies. Our finings not only provided dynamic mechanistic views of the iron competition but also highlighted the potential regulatory schemes in fungal pathogenesis.

overall_design: Each fish was intraperitoneally injected with C. albicans cells and these infected fish were collected at 0.5, 1, 2, 4, 6, 8, 12, 16, 18 hpi. 0.625μg of Cy3 cRNA for C. albicans array and 1.65 μg of Cy3 cRNA for zebrafish array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Each time points contain three biological repeat. For C. albicans array, each biological repeat has two technical replicates.

first: Yung-Jen

last: Chuang

first: Chung-Yu

last: Lan

first: Bor-Sen

first: Wen-Ping

last: Hsieh

first: David

middle: S

last: Wong


title: Knockdown of human TCF4 affects multiple signaling pathways involved in cell survival, epithelial-to-mesenchymal transition and neuronal differentiation

status: Public on Aug 20 2013

city: Cardiff

first: Derek

last: Blake

address: Hadyn Ellis Building, Maindy Road

department: MRC Centre for Neuropsychiatric Genetics and Genomics

institute: Cardiff University

summary: TCF4 is an important neurodevelopmental transcription factor associated with schizophrenia and Pitt-Hopkins syndrome. In this study, we used genome-wide expression profiling to determine the effects of acute TCF4 knockdown on gene expression in SH-SY5Y neuroblastoma cells. Pathway and enrichment analysis on the differentially expressed genes in TCF4-knockdown cells identified an over-representation of genes involved in TGF-β signaling, epithelial-to-mesenchymal transition (EMT) and apoptosis. Among the most significantly differentially expressed genes were the EMT regulators SNAI2 and DEC1 and the proneural genes NEUROG2 and ASCL1. Altered expression of several mental retardation genes such as UBE3A (AS), ZEB2 (MWS) and MEF2C was also found in TCF4-depleted cells. These data suggest that TCF4 regulates a number of convergent signaling pathways involved in cell differentiation and survival in addition to a subset of clinically important mental retardation genes.

overall_design: To identify TCF4-mediated gene expression changes in SH-SY5Y cells, experiments were conducted with two control (mock and GAPDH KD) and two TCF4 knockdown (KD1 and KD2) groups. Two non-overlapping siRNAs against TCF4 were designed and transfected over a 72h period to induce global knockdown of TCF4 transcripts. In parallel, cells were mock transfected (mock; transfection reagent only) and transfected with an unrelated siRNA against GAPDH (GAPDH KD) in order to control for background gene expression changes due to transfection, presence of dsRNA and activation of the cellular silencing machinery. After transfection, RNA was extracted from all cells, converted to cDNA and labelled for microarray hybridization. Each of the four treatment groups (mock, GAPDH KD, KD1 and KD2) contained three biological replicates which were processed at the same time using the Toray microarray platform.

first: Marc

middle: P

last: Forrest

first: Adrian

last: Waite

first: Enca

last: Martin-Rendon


title: miRNA expression in AML and healthy controls

status: Public on Aug 09 2013

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

summary:
Acute myeloid leukemia (AML) is a hematopoietic malignancy with a dismal outcome in the majority of cases. A detailed understanding of the genetic alterations and gene expression changes that contribute to its pathogenesis is important to improve prognostication, disease monitoring, and therapy. The expression of 636 human miRNAs was compared between samples from 52 patients with AML and 13 healthy individuals by locked nucleic acid (LNA) based microarray technology. 143 miRNAs were expressed at detectable levels, and  64 of these were significantly differentially expressed between AML and healthy peripheral blood, bone marrow, and/or CD34+ cells.
Reference: A Rommer et al, Overexpression of primary microRNA 221/222 in acute myeloid leukemia, BMC Cancer, 2013.

overall_design: 52 AML, 5 peripheral blood (PB), 5 bone marrow (BM), and 3 CD34+ cell samples from healthy donors were subjected to miRNA microarray analysis.

first: Hubert

last: Hackl

first: Christine

last: Schneckenleithner

first: Marcel

last: Scheideler

first: Peter

last: Valent

first: Heinz

last: Sill


title: Host and pathogen interaction: time course [zebrafish]

overall_design: Each fish was intraperitoneally injected with C. albicans cells and these infected fish were collected at 0.5, 1, 2, 4, 6, 8, 12, 16, 18 hpi. 0.625μg of Cy3 cRNA for C. albicans array and 1.65 μg of Cy3 cRNA for zebrafish array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Each time points contain three biological repeat. For C. albicans array, each biological repeat has two technical replicate.


title: Murine Cytomegalovirus Protein pM79 is a Key Regulator for Viral Late Transcription

status: Public on Jul 31 2013

city: Saint Louis

first: travis

last: Chapa

state: MO

address: 4440 Parkview Place

department: Microbiology

institute: Washington University in St. Louis

summary: We characterized the role of the conserved murine cytomegalovirus (MCMV) gene M79.  Using a recombinant MCMV virus carrying a tagged M79 coding sequence, we showed that M79 encoded a protein (pM79) which was expressed at late times of infection and localized to nuclear viral replication compartments.  M79 transcription was largely dependent on viral DNA synthesis but was markedly stimulated by pM79, suggesting a positive feedback loop.  To investigate its role, we created the recombinant virus SMin79, in which the M79 coding sequence was disrupted by an 88-nt insertion.  We subsequently repaired the mutation to generate marker-rescued virus SMrev79.  While SMrev79 grew efficiently in fibroblasts, SMin79 failed to produce infectious progeny but was rescued by pM79 expression in trans.  During SMin79 infection, representative viral immediate early and early gene products, as well as viral DNA, accumulated efficiently.  Formation of viral replication compartments also appeared normal.  Pulsed field gel electrophoresis analysis indicated that the overall structure of replicating viral DNA was indistinguishable in cells infected with SMin79 compared to that with wild type virus.  However, the accumulation of viral products for late gene M55 was severely compromised.  Viral oligonucleotide tiled array analysis revealed that the accumulation of many late transcripts, defined by their sensitivity to viral DNA synthesis inhibitor phosphonoacetic acid, was markedly reduced by pM79 mutation.  This study extends our previous work to suggest that cytomegaloviruses use a conserved mechanism to promote transcription at late stages of infection, and that pM79 regulates expression of a subset of viral DNA synthesis-dependent transcripts.

overall_design: This study consists of 4 unreplicated samples. RNA from Mock-infected, WT infected, WT infected in the presence of PAA, and a mutant M79 version of MCMV.

first: Travis

first: L

last: Johnson

first: Christopher

last: Affolter

first: Mark

middle: C

last: Valentine

first: Anthony

last: Fehr

first: Wayne

last: Yokoyama

first: Dong

last: Yu


title: Target specificity amongst canonical nuclear poly(A) polymerases in plants modulates organ growth and pathogen response

status: Public on Jul 29 2013

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

summary: Polyadenylation of pre-mRNAs is critical for efficient nuclear export, stability and translation of the mature mRNAs, and thus for gene expression. The bulk of pre-mRNAs are processed by canonical nuclear poly(A) polymerase (PAPS). Both vertebrate and higher-plant genomes encode more than one isoform of this enzyme, and these are co-expressed in different tissues. However, in neither case is it known whether the isoforms fulfil different functions or polyadenylate distinct subsets of pre-mRNAs. Here we show that the three canonical nuclear PAPS isoforms in Arabidopsis are functionally specialized due to their evolutionarily divergent C-terminal domains. A strong loss-of-function mutation in PAPS1 causes a male gametophytic defect, while a weak allele leads to reduced leaf growth that results in part from a constitutive pathogen response. By contrast, plants lacking both PAPS2 and PAPS4 function are viable with wild-type leaf growth. Polyadenylation of SMALL AUXIN UP RNA (SAUR) mRNAs depends specifically on PAPS1 function. The resulting reduction in SAUR activity in paps1 mutants contributes to their reduced leaf growth, providing a causal link between polyadenylation of specific pre-mRNAs by a particular PAPS isoform and plant growth. This suggests the existence of an additional layer of regulation in plant and possibly vertebrate gene expression, where the relative activities of canonical nuclear PAPS isoforms control de novo synthesized poly(A)-tail length and hence expression of specific subsets of mRNAs.

overall_design: Comparing inflorescences and seedlings from paps1-1 mutants and WT. 4 biological replicates for each genotype and tissue.

first: Son

last: Lang Vi

first: Gerda

last: Trost

first: Peggy

last: Lange

first: Hjördis

last: Czesnick

first: Nishta

last: Rao

first: Diana

last: Lieber

first: Thomal

last: Laux

first: William

last: Gray

first: James

last: Manley

first: Detlef

last: Groth

first: Christian

last: Kappel


title: TLR9 deficiency promotes CD73 expression in T cells and diabetes protection in NOD mice

status: Public on Jul 11 2013

city: New Haven

first: NINGWEN

last: TAI

state: CT

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University

summary: Analyze the effect of TLR9 deficiency on immue cell function at the gene expression level. Our hypothesis was that TLR9 deficiency promotes CD73 expression in T cells thus regulates autoimmune diabetes development in NOD mice.

overall_design: Sorted TCRb+ cells were pooled from several mice for furhter RNA extraction and cRNA labeling.

first: Li

last: Wen

first: Suan

middle: F

last: Wong

first: Ningwen

last: Tai


title: Expression data of LNCaP and MDA PCa 2b cells in absence or presence of IL6

status: Public on Aug 02 2013

city: Beerse

first: Tine

last: Casneuf

address: Turnhoutseweg 30

department: Oncology Translational Research

country: Belgium

institute: Janssen R&D

summary: Prostate cancer (PCa) development and progression are associated with chronic inflammation. The cytokine interleukin (IL)-6 can influence progression, differentiation, survival, and angiogenesis of PCa. To identify novel pathways that are triggered by IL-6, we performed a gene expression profiling of two PCa cell lines, LNCaP and MDA PCa 2b, under treatment with 5 ng/ml IL-6. Interferon regulatory factor (IRF)9 was identified as one of the most prevalent IL-6 regulated genes in both cell lines. IRF9 is a mediator of type I interferon signaling and acts together with signal transduction and activator of transcription (STAT)1 and 2 to activate transcription of interferon responsive genes. The IL-6 regulation of IRF9 was confirmed at mRNA and protein levels by quantitative real-time PCR and Western blot, respectively, in both cell lines and could be blocked by the anti-IL-6 antibody Siltuximab. Three PCa cell lines with an autocrine IL-6 loop, PC3, DU145, and LNCaP-IL-6+, showed a high expression of IRF9. A tissue microarray with 36 malignant and adjacent 36 benign areas from prostate cancer specimens showed that IRF9 protein expression is moderately elevated in malignant areas and positively correlates with the tissue expression of IL-6. Downregulation and overexpression of IRF9 provided evidence for an interferon-independent role of IRF9 on cellular proliferation of different PCa cell lines. Furthermore, expression of IRF9 was essential to mediate the antiproliferative effects of IFN-α2. We concluded that IL-6 is an inducer of IRF9 expression in prostate cancer and a sensitizer for the antiproliferative effects of IFNα2.

overall_design: LNCaP and MDA PCa 2b cells were seeded in 12 wells each. The cells were starved for 24 h and half were treated with 5 ng/ml IL-6 for 18 h. Two biological replicates were performed, each in three replicates, resulting in 12 samples per cell line.

first: Holger

middle: H

last: Erb

first: Regina

middle: V

last: Langlechner

first: Patrizia

last: Moser

first: Florian

last: Handle

first: Tineke

first: Karin

last: Verstraeten

first: Bettina

last: Schlick

first: Georg

last: Schäfer

first: Brett

last: Hall

first: Kate

last: Sasser

first: Zoran

last: Culig

first: Frédéric

last: Santer


title: The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter proximal nucleosomes [array]

status: Public on Jul 08 2013

city: Augusta

first: Wei-Hua

last: Wu

state: GA

address: 1462 Laney Walker Blvd

department: Neurology

institute: IMMAG/MCG/GRU

summary: The evolutionarily conserved ATP-dependent chromatin remodeling enzyme Fun30 has recently been shown to play important roles in heterochromatin silencing and DNA repair. However, how Fun30 remodels nucleosomes is not clear. Here we report a nucleosome sliding activity of Fun30 and its role in transcriptional repression. We observed that Fun30 repressed the expression of genes involved in amino acid and carbohydrate metabolism, the stress response, and meiosis. In addition, Fun30 was localized at the 5′ and 3′ ends of genes and within the open reading frames of its targets. Consistent with its role in gene repression, we observed that Fun30-target genes lacked histone modifications often associated with gene activation and showed an increased level of ubiquitinated histone H2B. Furthermore, genome-wide nucleosome mapping analysis revealed that the length of the nucleosome-free region at the 5′ end of a subset of genes was changed in Fun30-depleted cells. In addition, the positions of the -1, +2 and +3 nucleosomes at the 5′ end of target genes were significantly shifted, while position of the +1 nucleosome remained largely unchanged in the fun30Δ mutant. Finally, we demonstrated that affinity purified single-component Fun30 exhibited nucleosome sliding activity in an ATP-dependent manner. These results define a role for Fun30 in regulation of transcription and indicate that Fun30 remodels chromatin at the 5′ end of genes by sliding promoter proximal nucleosomes.

overall_design:
Data sets for each strain were generated from three biological replicates and experimental dye swap duplicates of each replicate.
The six wildtype raw data files linked below were used to generate normalized, log2 (mutant/WT) ratios for all 3 Samples.

first: Boseon

last: Byeon

first: Wei

last: Wang

first: Artem

last: Barski

first: Ryan

middle: T

last: Ranallo

first: Kan

last: Bao

first: Dustin

last: Schones

first: Keji

last: Zhao

first: Carl


title: Expression from Staphylococcus aureus strain USA300-lac during low and 2M NaCl exposure

status: Public on Jul 01 2013

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
S. aureus has the propensity to survive a range of NaCl challenge conditions
We used commercially available Affymetrix S. aureus GeneChips (part number 900514) to compare the gene expression properties of wild type cells during growth at no or high (2M) NaCl.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: S. aureus strain USA300-lac cells were grown to late exponential phase growth in the absence or presence of 2M NaCl, total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the regulatory effects of high NaCl.

first: Terry

last: Krulwich


title: Rapid clearance of PcG histone modifications from Hox genes anticipates motor neuron differentiation: ChIP-chip

status: Public on Jul 04 2013

city: University Park

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary:
[original Title] Rapid and synchronous clearance of PcG histone modifications from Hox genes anticipates motor neuron differentiation.
Hox genes are expressed in patterns that are spatially and temporally collinear with their chromosomal organization. This feature is an evolutionarily conserved hallmark of embryonic development, and in vertebrates it is critical, among others, for the specification of motor neuron subtypes and the wiring of sensory-motor circuits.  We show here that the differentiation of motor neurons from stem cells is accompanied by a synchronous, domain-wide clearance of “repressive” Polycomb (PcG)-dependent histone methylation from Hox gene chromatin domains.  These findings argue against the idea, advanced recently, that the collinear dynamics of Hox gene expression invariably reflects the progressive clearance of repressive chromatin modifications.  The rapid establishment of stable chromatin domains in response to a transient patterning signal likely serves as a molecular correlate of enduring rostro-caudal neural identity, which underlies the specification of postmitotic motor neuron subtype diversity and neuronal circuit assembly.

overall_design: The differentiation of ventral motor neurons is induced by treating embryonic stem cell cultures with retinoic acid and hedgehog agonist. Here, ChIP-chip using a custom Agilent array is used to profile the occupancy of H3K27me3, H3K4me3, and H3K79me2 at various defined stages during the differentiation process.

first: Esteban

middle: O

last: Mazzoni

first: Scott

last: McCuine

first: Timothy

middle: W

last: Danford

first: Christopher

last: Reeder

first: P

last: Rolfe

first: Robin

last: Dowell

first: Seraphim

last: Thornton

first: Laurie

last: Boyer

first: Richard

last: Young

first: David

middle: K

last: Gifford

first: Hynek

last: Wichterle


title: EGFRvIII vs. Control - xenograft glioblastomas

city: Los Angeles

first: Erik

last: Anderson

state: CA

address: 6-567 MRL, 675 Charles E. Young Drive South

department: MBIDP

institute: UCLA

summary:
Glioblastoma cell lines were xenografted onto mice and resulting tumors were profiled by microarray.
Xenograft recipient mice were NOD/SCID/gamma (NSG) male mice 3 months old.

overall_design: In this set, 6 total samples were analyzed.  There were three biological replicates for each of two conditions:  EGFRvIII containing tumors and control.  Arrays were analyzed for gene expression using GeneBase and for alternative splicing using MADS+ software.

first: Ivan

last: Babic

first: Douglas

last: Black

last: Mischel


title: Wapl controls higher-order chromatin structure in interphase chromosomes (gene expression)

first: Roman

last: Stocsits

address: Campus-Vienna-Biocenter 1

institute: IMP - Research Institute of Molecular Pathology

summary: Mammalian genomes contain several billion base pairs of DNA which are packaged in chromatin fibers. At selected gene loci, cohesin complexes have been proposed to arrange chromatin fibers into higher-order structures, but it is poorly understood how cohesin performs this task, how important this function is for determining the structure of chromosomes, and how this process is regulated to allow changes in gene expression. Here we show that the cohesin release factor Wapl controls chromatin structure and gene regulation at numerous loci throughout the mouse genome. Conditional deletion of the Wapl gene leads to stable accumulation of cohesin on chromatin, chromatin compaction, altered gene expression, cell cycle delay, chromosome segregation defects and embryonic lethality. In Wapl deficient chromosomes, cohesin accumulates in an axial domain, similar to how condensins form a “scaffold” in mitotic chromosomes. We propose that Wapl controls chromatin structure and gene regulation by determining the residence time with which cohesin binds to DNA.

overall_design: 4 biological replicates for each genotype (Wapl +/F; Wapl -/F) treated with/without 4-OHT =16 samples

first: Annelie

last: Wuensche

first: Erika

last: Schirghuber

first: Gordana

last: Wutz

first: Jan

last: Ellenberg

first: Jan-Michael

last: Peters

first: Markus

last: Jaritz

first: Sébastien

last: Huet

first: Tomoko

last: Nishiyama

first: Bhaskara

last: Venugopal

first: Antonio

last: Tedeschi


title: Expression data from human Jurkat T cells exposed to 31 compounds

status: Public on Jul 22 2013

city: Wageningen

first: Jia

last: Shao

address: Akkermaalsbos 2

department: TE

country: Netherlands

institute: RIKILT-Institute of food safety

summary:
Compounds with direct immunotoxic properties, including metals, mycotoxins, agricultural pesticides and industrial chemicals, form potential human health risks due to exposure through food, drinking water, and the environment. Insights into the mechanisms of action are currently lacking for the majority of these direct immunotoxicants. Therefore, the present work aimed to gain insights into the molecular mechanisms underlying direct immunotoxicity. To this end, we assessed in vitro the effects of 31 test compounds on the transcriptome of the human Jurkat T cell line. These compounds included direct immunotoxicants, immunosuppressive drugs with different mode of actions, and non-immunotoxic control chemicals. Pathway analysis of the microarray data  allowed us to identify canonical pathways and Gene Ontology processes that were transcriptionally regulated in common by immunotoxicants (i) with structural similarities, such as the tributyltins TBTC and TBTO that activated the retinoic acid / X receptor (RAR / RXR) signaling pathway, and (ii) without structural similarities, such as As2O3, DBTC, diazinon, MeHg, ochratoxin A, S9 treated ochratoxin A, S9 treated cyclophosphamide, and S9 treated benzo[a]pyrene, that activated unfolded protein response, and FTY720, lindane, and propanil, that activated the cholesterol biosynthesis pathway. In addition, processes uniquely affected by individual immunotoxicants were identified, such as the induction of Notch receptor signaling and the down regulation of acute phase response genes by ochratoxin A. These findings were validated by quantitative Real-Time PCR (Q-RT-PCR) analysis of genes involved in these processes. Our study indicated that diverse modes of action are involved in direct immunotoxicity and  that a set of pathways or genes, rather than one single gene can be used to screen compounds for direct immunotoxicity.
We used microarrays to study the gene expression changes in Jurkat cells upon exposure to various immunotoxicants and identified distinct pathways related with chemical-induced direct immunotoxicity.

overall_design: Jurkat cells were exposed to 31 compounds. The exposure experiments were done on four different days, with four different passages of Jurkat cells. Therefore, for each compound, we have four biological replicates. DMSO was used as the carrier control for all the samples. In total, 128 samples (including four untreated cell samples) were analyzed and will be uploaded. All the data were normalized by the average of the carrier control (DMSO).

first: Madhumohan

last: Katika

first: Peter

last: Schmeits

last: Hendriksen

first: Henk

last: van Loveren

first: Ad

last: Peijnenburg

first: Oscar

last: Volger


title: Characterization of four TCE-dechlorinating microbial enrichments grown with different cobalamin stress and methanogenic conditions

status: Public on Jun 30 2013

city: Urbana

first: Yujie

last: Men

address: 205 N Mathews Ave

institute: University of Illinois at Urbana-Champaign

summary: Four stable and robust TCE-dechlorinating microbial communities were enriched from TCE-contaminated groundwater under four different conditions exploring two parameters, high and low methanogenic activity (Meth and NoMeth), with and without vitamin B12 supplement  (MethB12 and NoMethB12, Meth and NoMeth, respectively).  Identical amounts of lactate (2.7 mmol) and TCE (20 μl) were supplied as electron donor and electron acceptor.  All four cultures were capable of reductively dechlorinating TCE to VC and ethene.  Genomic DNA of the four enrichments was applied on a quad-Dhc-genome microarray in order to characterize the gene content of Dehalococcoides species present in the four enrichments

sample_organism:
environmental samples
environmental samples
environmental samples

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

overall_design: The genomic DNA of four enrichment cultures completely dechlorinated TCE to VC and ethene was used on the microarray to query Dehalococcoides species present in the mixed cultures.

first: Patrick

last: Lee

first: Katie

last: Harding

first: Lisa

last: Alvarez-Cohen


title: Control of Reproductive Floral Organ Identity Specification in Arabidopsis by the C Function Regulator AGAMOUS (expression)

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD

summary:
Characterization of the activities of the transcription factor that AG encodes throughout flower development using perturbation assays in combination with a floral induction system (FIS) that allows a stage-specific analysis of flower development.
The series contains static perturbation experiments (null allele ag-1), and amiRNA knockdown experiments.

overall_design: Two conditions (i.e. perturbation experiments of ag-1 homozygous in the FIS vs ag-1 heterozygous in the FIS across three developmental stages. amiRNA knockdown experiments induced amiRNA expression vs. uninduced.

first: Diarmuid

last: Ó’Maoiléidigh

first: Samuel

last: Wuest

first: Andrea

last: Raganelli

first: Frank

last: Wellmer


title: MiR-210 is induced by Oct-2, regulates B-cells and inhibits autoantibody production

status: Public on Jun 21 2013

city: Cambridge

first: Yingting

last: Mok

address: Hills Road

department: Cambridge Institute for Medical Research

institute: University of Cambridge

summary: MicroRNAs are small, non-coding RNAs that regulate gene expression post-transcriptionally. Here, we show that miR-210 is induced by Oct-2, a key transcriptional mediator of B-cell activation. Germline deletion of miR-210 results in the development of autoantibodies from 5 months of age. Overexpression of miR-210 in vivo resulted in cell autonomous expansion of the B1 lineage and impaired fitness of B2 cells. Mice over-expressing miR-210 exhibited impaired class-switched antibody responses, a finding confirmed in wild-type B-cells transfected with a miR-210 mimic.  In vitro studies demonstrated a defect in cellular proliferation and cell-cycle entry, which was consistent with the transcriptomic analysis demonstrating down-regulation of genes involved in cellular proliferation and B cell activation. These findings indicate that Oct-2 induction of miR-210 provides a novel inhibitory mechanism for the control of B cells and autoantibody production.

overall_design:
Splenic B-cells from different mouse strains were stimulated with either anti-IgM, CD40L and IL-4 or LPS for 48 hours
Treatments: rest (unstimulated), Fab/Fab2 (=anti-IgM + CD40L + IL-4), LPS.  There is no difference between Fab and Fab2 stimulation conditions.
The goal of this study was to look for activation-induced microRNA changes upon B-cell activation, of which miR-210 was one of them.


title: Genome and transcriptome adaptations of S. Typhimurium

status: Public on Jun 19 2013

first: Robert

last: Kingsley

address: Hinxton

institute: The wellcome Trust Sanger Institute

summary: Part of a study to determine the impact of genome evolution on host adaptation of a group of Salmonella Typhimurium. The experiment is designed to determine the impact of culture at elevated temperature on gene experssion.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: strains SL1344 and 94-213 at 37 and 42C

middle: A


title: Dysregulated microRNAs in sapje and sapje-like zebrafish

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary:
MicroRNAs were isolated from wild type (SW and SLW; sapje-wild type littermates, sapje-like-wild type littermates) and sapje and sapje-like fish at 5 and 30 days post fertilization (dpf)
Comparison of wildtype and sapje and sapje-like fish at 5 and 30 dpf to identify commonly dysregulated microRNA biosignature

overall_design: This experiment includes 2 groups per cohort (SW1, 2 vs S1, S2 at 5 and 30 dpf) and (SLW1,2 vs SL1, 2 at 5 and 30 dpf)

first: Louis

middle: M

last: Kunkel

first: Matthew

last: Alexander

first: Iris

last: Eisenberg

first: Genri

last: Kawahara


title: Microarray gene expression profiling of neural tissues in bovine spastic paresis

status: Public on Jun 07 2013

city: Viterbo

first: Alessio

last: Valentini

address: via San Camillo de Lellis

department: IBAF

country: Italy

institute: University of Tuscia

summary:
Background
Bovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both limbs and is associated with a scarce increase in body weight. This disease seems to be caused by an autosomal and recessive gene, with incomplete penetration, although no genes clearly involved with its onset have been so far identified. We employed cDNA microarrays to identify metabolic pathways affected by BSP in Romagnola cattle breed. Investigation of those pathways at the genome level can help to understand this disease.
Results
Microarray analysis of control and affected individuals resulted in 268 differentially expressed genes. These genes were subjected to KEGG pathway functional clustering analysis, revealing that they are predominantly involved in Cell Communication, Signalling Molecules and Interaction and Signal Transduction, Diseases and Nervous System classes. Significantly enriched KEGG pathway’s classes for the differentially expressed genes were calculated; interestingly, all those significantly under-expressed in the affected samples are included in Neurodegenerative Diseases. To identify genome locations possibly harbouring gene(s) involved in the disease, the chromosome distribution of the differentially expressed genes was also investigated.
Conclusions
The cDNA microarray we used in this study contains a brain library and, even if carrying an incomplete transcriptome representation, it has proven to be a valuable tool allowing us to add useful and new information to a poorly studied disease. By using this tool, we examined nearly 15000 transcripts and analysed gene pathways affected by the disease. Particularly, our data suggest also a defective glycinergic synaptic transmission in the development of the disease and an alteration of calcium signalling proteins. We provide data to acquire knowledge of a genetic disease for which literature still presents poor results and that could be further and specifically analysed in the next future. Moreover this study, performed in livestock, may also harbour molecular information useful for understanding human diseases.

overall_design: Samples of spinal cord from 4 affected and 4 control individuals of the Romagnola breed were collected immediately after slaughtering and later stored in RNA (Sigma-Aldrich). Dye-swaps were performed using pooled cDNA probes from the 4 control animals and the 4 affected animals.

first: Lorraine

last: Pariset

first: Silvia

last: Bongiorni

first: Susana

last: Bueno

first: Cesare

last: Gruber

first: Gianluca

last: Prosperini

first: Giovanni

last: Chillemi

last: Bicorgna

first: Arcangelo

last: Gentile


title: Gene expression changes associated with KIAA1199 expression in SW480 cells

status: Public on Jun 01 2013

city: Zurich

first: Michal

last: Okoniewski

state: Zurich

address: Binzmühlestrasse 130

country: Switzerland

institute: ETH Zurich

summary: The aim was to identify gene expression changes upon expression of KIAA1199 in a colon cancer cell line.

overall_design: Inducible expression of KIAA1199A was achieved with a two-step procedure. First, SW480 cells were transfected with the pcDNA6TR vector (Invitrogen) and the tetracycline repressor-expressing cells selected with 7 μg/ml blasticidin S (InvivoGen).  The blasticidin-resistant cells were then transfected with the pT-Rex-DEST30-KIAA1199 construct (see below) and selected with 0.4 mg/ml G418.  The growth medium used for these cells was supplemented with 10% Tet-system-approved fetal calf serum (Biochrom).

first: Giancarlo

last: Marra

first: Amit

last: Tiwari


title: Identification of genes essential for Moraxella catarrhalis growth under iron-limiting conditions

status: Public on Jun 06 2013

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

institute: Radboud University Medical Centre

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Study of UVB responses of SV40 transformed human lung fibroblast: Control vs. UVB irradiated

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

institute: nthu

summary: Previous studies showed that SV40 transformed cells have unique DNA damage responses; further inspecting these responses by microarray provides an opportunity to discover transciprtional insights of DNA damage responses after UVB irradiation. This study is used to comapre to GSE7589, our previous study of human normal lung fibroblast after UVB irradiation.

overall_design: We used a loop design in this study, cDNA microarray experiment consisted of eight RNA samples, including UVB-irradiated samples and their corresponding controls of 4 time points after UV irradiation.

first: Cheng-Wei

first: Ian

last: Hsu


title: Identification of genes essential for Moraxella catarrhalis growth under iron-limiting conditions using Genomic Array Footprinting (GAF)

summary: Iron-sequestration by the human host is a first line defense against respiratory pathogens like Moraxella catarrhalis, which consequently experiences a period of iron-starvation during colonization and infection. We determined the genetic requirements for M. catarrhalis growth during iron-starvation using the high-throughput genome-wide screening technology genomic array footprinting (GAF). To this end, a large marinerT7 transposon mutant library (~28,000 independent transposon mutants) was grown under iron-limiting conditions, achieved by sequestration of iron by 30 µM Desferal (DF30), and under control growth conditions (brain heart infusion broth, DF0). Mutants were recovered at exponential- and the early-stationary growth phase and used for the generation of mutant-specific cDNA probes that were hybridized to custom-designed NimbleGen GAF microarrays. The results described in this study are further discussed in Stefan P.W. de Vries, Peter Burghout, Jeroen D. Langereis, Aldert Zomer, Peter W.M. Hermans, Hester J. Bootsma: Genetic requirements for Moraxella catarrhalis growth under iron-limiting conditions, Molecular Microbiology.

overall_design: cDNA probes generated from mutants recovered during the exponential growth phase, or early-stationary phase under challenge (iron-limiting, DF30) or control conditions (DF0). Hybridization on GAF 4x72K custom design Nimblegen GAF arrays for read-out.

first: Stefan

last: de Vries

first: Peter

last: Burghout

first: Jeroen

middle: D

last: Langereis

first: Aldert

last: Zomer

last: Hermans


title: Human plasma: circulating microRNA after acute resistance exercise

status: Public on Jun 29 2013

city: Tokyo

first: Takayuki

last: Akimoto

address: Hongo 7-3-1

country: Japan

institute: The University of Tokyo

summary: Profiling of circulating miRNAs before, 60 mins, 1day and 3 days after an acute resistance exercise.

overall_design: Three subjects performed an acute resistance exercise. The resistance exercise consisted of two consecutive exercises (bench press and bilateral leg press), consisting of five sets of 10 repetitions at 70% of 1 RM. The subjects were allowed to rest for 1 min between each set and exercise. The subjects were instructed to lift and lower the load at a constant velocity, taking about 2 s for each repetition. If the load became too heavy, the subject was assisted. The range of motion in each exercise was from 90° to 0° (0° at full extension). Blood samples were taken before, 60 mins, 1day and 3days after the exercise.


title: WT vs MO-grnA injected: 16, 24, 48, 72 hpf trunk region of zebrafish embryos

city: Taipei

first: gen

middle: hwa

last: lin

state: Nankang

address: 128,section2,academia road

department: Institute of Cellular and Organismic Biology

institute: Academia Sinica

summary: Transcriptional profiling of zebrafish embryo comparing wild type untreated embryos with embryos injected with morpholino of zf-grna. This assay is used for determination of expression profiling of trunk muscle at 16, 24, 48, 72 hpf under GRN-A deficiency.

overall_design: Two-condition experiment, wild type vs. MO-grnA treated cells. Biological replicates: each group contains 200 embryos.

first: Yen-Hsing

last: Li

first: Gen-Hwa

last: Lin

first: Jen-Leih

last: Wu


title: How nanomolar doses of combined metal salts (Cd, Cu, Hg) induce DNA damage and transcriptional changes in the gills of Mytilus galloprovincialis.

city: Padova

first: Laura

last: Varotto

address: via U. Bassi 58/3

department: Biology Department

institute: University of Padova

summary: We used a cDNA microarray previously defined for the marine sentinel organism Mytilus galloprovincialis (MytArray1.0) to evaluate the effects of nanomolar doses of combined metal salts (50, 100 and 200 nM mixtures of Cd, Cu and Hg) after 48 hours of mussel exposure. Pointing to the mussel gills, first target of toxic water contaminants and actively proliferating tissue, we found significant dose-related increases of cells with micronuclei and other nuclear abnormalities in the treated mussels, with differences in the bioconcentration of the three metals determined in the mussel pulp by atomic absorption spectrometry. Following gill RNA purification and DNA microarray analysis, individual gene expression profiles revealed some transcriptional changes at the 50 nM dose, and substantial increases of differentially expressed genes at the 100 and 200 nM doses with roughly similar amounts of up- and down-regulated signals. The functional annotation of transcripts with consistent expression trends and significantly altered at least in one dose point disclosed the complexity of the induced cell response.

overall_design: Three-condition experiment (50, 100 and 200 nM doses), individual treated mussel vs. pooled control mussels (N=5), 3 biological replicates with dye-swap competitive hybridization (array A and B, 2 technical replicates/array).

first: Umberto

last: Rosani

first: Paola

last: Venier


title: Systems Biology approach to identify transcriptome reprogramming in Arabidopsis thaliana during insect and bacterial attack (Brevicoryne brassicae)

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. Defense responses and networks, unique and specific for aphid or Pseudomonas  stresses were identified. Our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and thus opened up a new direction to conduct large-scale targeted experiments to explore detailed regulatory links among them. The presented results provide a first comprehensive understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at a systems biology level.

overall_design: Arabidopsis thaliana (ecotype Colombia-0) seeds were grown in 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite), 3 plants per pot. Plants were kept in growth chambers Vötsch VB 1514 (Vötsch Industrietechnik GmbH, Germany) under the following conditions: a 16/8 h (light/dark) photoperiod at 22°C/18°C, 40%/70% relative humidity, and 70/0 μmol m-2s-1 light intensity. After 32 days plants had 8 fully developed leaves. Each plant was infested with 32 wingless aphids [Brevicoryne Brassicae] (4 per leaf), which were transferred to leaves with a fine paintbrush. Infested plants and aphid-free controls were kept in plexiglass cylinders. Plants were harvested 72 h after infestation between the 6th and 8th hour of the light photoperiod. Four biological replicates were prepared from aphid infested and control plants, each sampled from 15 individual plants. Whole rosettes were cut at the hypocotyls and aphids were removed by washing with Milli-Q-filtered water. Differences in transcriptional responses were measured by comparing genes expression of aphid infested plants against non-infested control plants.

first: Anna

last: Kuśnierczyk

first: Torfinn

last: Sparstad

first: Pankaj

last: Barah

first: Atle

last: Bones


title: Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells: Expression Moraxella catarrhalis strain BBH18 during adherence to human phanryngeal epithelial Detroit 562 cells

status: Public on Jun 27 2013

first: Hester

last: Bootsma

summary: During the course of infection, respiratory pathogens like Moraxella catarrhalis needs to adhere to epithelial cells of different host niches such as the nasopharynx and lungs. Consequently, efficient adhesion to epithelial cells is considered an important virulence trait of M. catarrhalis.  We examined the interaction between human pharyngeal epithelial Detroit 562 cells and M. catarrhalis BBH18 during adherence using a combination of Tn-seq, a genome-wide negative selection screenings technology, and expression profiling of both host and pathogen. The results described in this study are further discussed in Stefan P.W. de Vries, Marc J. Eleveld, Peter W.M. Hermans, Hester J. Bootsma: Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells, submitted.

overall_design: After 1 hour adherence to Detroit 562 cells, RNA was isolated from adherent (n = 4) and non-adherent (planktonic) (n = 4) M. catarrhalis BBH18 as well as from bacteria incubated in the infection medium alone (n = 3). RNA obtained from the adherent fraction was enriched for bacterial RNA using the MICROBEnrich kit (Ambion). Total RNA was labeled according to standard Nimblegen gene expression array protocols and hybridized to a 4x72K Nimblegen M. catarrhalis expression array for read-out.

first: Stefan

last: de Vries

first: Marc

middle: J

last: Eleveld


title: miR-106a-5p inhibits the proliferation and migration of astrocytoma cells and promotes apoptosis by targeting FASTK

status: Public on Jun 08 2013

city: Changzhou

first: Yilin

last: Yang

state: Jiangsu

address: 185#, Juqian Road

department: Modern Medical Research Center

country: China

institute: Third Affiliated Hospital of Soochow University

summary:
mRNA microarray experiments were performed to measure global mRNA expression in the presence of increased or decreased miR-106a-5p levels to to identify the total transcripts regulated by miR-106a-5p directly or indirectly.
FASTK was identified as a direct target gene of miR-106a-5p.

overall_design: In order to identify the total transcripts regulated by miR-106a-5p directly or indirectly, we first measured the global mRNA expression change through mRNA microarray by overexpressing or knocking down miR-106a-5p in cancer cells. Next, we combined bioinformatics programs to select candidate miR-106a-5p targets from the differentially regulated genes to refine the number of miR-106a-5p targets. Then we validated the miR-106a-5p target gene through western blot analysis, quantitative real-time PCR and luciferase reporter assay.

first: Feng

last: Zhi


title: Functional analysis of transcriptome dynamics during growth in Angus cattle longissimus muscle

first: Sonia

middle: Josefina

last: Moisá

state: IL

address: 1207 W. Gregory Dr.

department: Animal Sciences

institute: University of Illinois

summary: The bovine transcriptome dynamics in logissimus muscle (LM) during the post-natal growth remain unknown. Biopsies of LM from Angus steers were harvested at 0, 60, 120, and 220 d from early-weaning. A 13,153 bovine oligonucleotide array was used for transcript profiling. Functional analysis of microarray data was performed using the Dynamic Impact Approach (DIA) by means of KEGG and DAVID databases. During the growing phase, most of the highly-impacted pathways (e.g. Ascorbate and aldarate metabolism, Drug metabolism - cytochrome P450 and Retinol metabolism) were inhibited. The finishing phase, was characterized with the most striking differences with 3,784 differentially expressed genes (DEG; FDR <0.01). The functional analysis of those DEG revealed that the most-impacted KEGG canonical pathway was “Glycosylphosphatidylinositol (GPI) - anchor biosynthesis”. The inhibition of this pathway suggested a unique role of GPI-anchor proteins in intracellular trafficking during the finishing phase. A mechanism regulating muscle growth during the finishing phase was uncovered in which inhibition of calpastatin and activation of tyrosine aminotransferase ubiquitination promote proteasomal degradation, while the concurrent activation of ribosomal proteins promotes protein synthesis, thus, the balance of these processes likely results in a steady state of protein turnover during the finishing phase. Overall, results underscored the importance of transcriptome dynamics in LM to support key biological functions during rapid growth.

overall_design: The study utilized a subset of 14 animals from a larger study encompassing 32 purebred Aberdeen Angus steers from the University of Illinois beef cattle herd.  Steer calves were early-weaned (134 ± 10 d age) and after weaning were placed on a diet of 85% corn silage and 15% wet distiller’s grains (as-fed basis) for 3 wk. Subsequently, one half of Angus (n = 16) steers was randomly assigned to a high-byproduct or high-grain diet for a 112 d growing phase. The high-byproduct diet contained (dry matter basis) 35% corn silage, 20% corn gluten feed, 38% soyhulls, 3% cracked corn, and 3% soybean meal (49% crude protein). The high-grain diet contained 20% corn silage, 68% cracked corn, and 11% soybean meal (49% crude protein). Both diets contained 1% limestone/dicalcium phosphate/mineral/vitamin/urea/dry molasses mixture. Calculated NEG for the high-byproduct diet was 1.19 Mcal/kg and 1.43 Mcal/kg for the high-grain diet. At the end of the growing phase, steers on each group were fed “step-up diets” for 10 d. Step-up diet for high-byproduct-fed steers contained 1.37 Mcal NEG/kg. Step-up diet for high-grain-fed steers contained 1.43 Mcal NEG/kg but contained distiller’s dried grains (16% of dry matter). After the “step-up” period, all steers were finished on a common high-grain finishing diet containing 1.44 Mcal NEG/kg (15% corn silage, 58% cracked corn, 25% dried distiller’s grains, 1% limestone, and 1% urea/mineral/vitamin mixture). All diets were offered on an ad libitum basis. Steers had an individual electronic identification ear tag and individual feed intake data were collected using the GrowSafe system (GrowSafe Systems Ltd., Alberta, Canada). Cattle were harvested at approximately 13 mo age. A bovine oligonucleotide (70-mers) microarray with >13,000 annotated sequences developed at the University of Illinois, was used for transcript profiling.  Details on the development, annotation, and use of this microarray have been reported previously by Loor et al., 2007 (http://physiolgenomics.physiology.org/content/32/1/105.abstract).  Methods for microarray hybridization and scanning were as reported by Loor et al. (2007).  Briefly, slides were hydrated, dried, and placed in a UV Stratalinker 1800 (Stratagene, La Joya, CA) for ~5 min.  Slides were washed with 0.2% SDS solution, rinsed with MilliQ (Millipore) H2O, and placed in warm prehybridization soln for 45 min at 42 C. The same amount of Cy3- or Cy5-labelled cDNA from muscle and a reference standard RNA pool (made of different bovine tissues) were co-hybridized using a dye-swap design (i.e., two microarrays per sample).  Slides were incubated for 48 h at 45 C prior to scanning. Criteria for evaluation of slide quality included: identification of number of spots with a minimum median signal intensity of 3 SD above background; keeping slides with a minimum of 20,000 spots with minimum median signal intensity of 3 SD above background in both Cy3 and Cy5 channels; and keeping slides with a minimum mean intensity of 400 relative fluorescent units in both Cy3 and Cy5 channels across the entire slide. Data from a total of 112 microarrays were normalized for dye and microarray effects (i.e., Lowess normalization and microarray centering) and used for statistical analysis. Data were analyzed using the Proc MIXED procedure of SAS (SAS, SAS Inst. Inc., Cary, NC).  Fixed effects were treatment (high-byproduct, high-grain) and time (0, 56, 120, and 220 d), and dye.  Random effects included steer and microarray.  A covariate adjustment was used to assess treatment and treatment × time interactions, but time effects on gene expression were assessed without covariate adjustment.  Raw P values were adjusted using Benjamini and Hochberg’s false discovery rate (FDR). Differences in relative expression due to treatment × time interactions were considered significant at an FDR-adjusted P < 0.25 or at P < 0.01 for time effects.  qPCR data were normalized using the median of 4 suitable internal control genes, and were analyzed using the same statistical model described above.  Differences were considered significant at P-value of 0.05.

first: Daniel

last: Shike

middle: E

last: Graugnard

first: Sandra

middle: L

last: Rodriguez-Zas

first: Robin

last: Everts

first: Harris

last: Lewin

first: Dan

middle: B

last: Faulkner

first: Larry

last: Berger

first: Juan

last: Loor


title: To study gene expression by xylose fermenting strains in the presence and absence of furfural

city: Kobe

first: Akihiko

last: Kondo

address: 1-1 Rokkodai, Nada

department: Chemical Science and Engineering

institute: Kobe University

summary: The main objective is to develop a strain tolerant to furfural for ethanol production from lignocellulosic hydrolysates. We compare gene expressions among three genetically modified S. cerevisiae (control, TAL-expressing and TAL-ADH expressing strain) under the presence and absence of furfural.

overall_design: Samples for 3 strains (control, TAL-expressing and TAL-ADH expressing strain) were taken after 6h of exposure to furfural. Furfural concentration were 0 and 70 mM. Each samples were duplicated resulting in total of 12 samples.

first: Tomohisa

last: Hasunuma

first: Yumiko

last: Nambu

first: Ku

last: Syahidah

last: Ismail


title: Comprehensive expression analyses of neural cell type-specific miRNAs  identify new determinants of the specification and maintenance of neuronal phenotypes.

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

summary: We performed microarray profiling of miRNA expression across the four principal cell types of the central nervous system: neurons, astrocytes, oligodendrocytes and microglia, isolated from rat cortex. Our microarray results showed that the four cell types differ extensively in their miRNA expression. Over one third of the 351 miRNAs examined had higher than 5-fold differences in expression between two of the four cell types. As expected, cell types of common developmental origin differed least in their miRNA expression profiles (astrocytes and oligodendrocytes), while neurons and microglia showed more unique miRNA expression profiles. 63 miRNAs showed cell type specific enrichment (39 miRNAs) or depletion (24 miRNAs) when comparing the four cell types using criteria of a minimum 5-fold difference in expression in one cell type compared to the average expression in the other three and minimum 2-fold change compared to each of the other three types individually and a false positive rate (FDR) p value lower than 0.01. When comparing only neurons, astrocytes and oligodendrocytes 115 miRNAs were specifically enriched (89 miRNAs) or depleted (36 miRNAs) in one cell type.

overall_design: Genome-wide profiling comparing miRNA expression between mature neurons, astrocytes, oligodendrocytes and microglia. Three to four biological replicates per cell type were analyzed.

first: Ana

last: Jovicic

first: Ruth

last: Luthi-Carter


title: Rhesus monkeys challenged with H. pylori and ENNG

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

summary: Gene expression was studied in samples from the stomach of Rhesus monkeys that have been infected with Helicobacter pylori and treated with a known carcinogen (Ethyl-nitro-nitrosoguanidine (ENNG)) that is similar to known nitrosamine dietary carcinogens. The samples represent the following: Biopsy 4689 is from animal 81G taken 55 months after inoculation with H. pylori and the start of the carcinogen ENNG Biopsy 4691 is from animal 63G taken 55 months after inoculation with H. pylori and the start of the carcinogen ENNG Biopsy 4709 is from animal 92F taken after 55 months of observation and no treatment (control). Gastric biopsies were obtained at the indicated times and RNA was harvested from the sample. All hybridizations were conducted against a common reference that was prepared using commercially obtained RNA isolated from the stomach of uninfected monkeys.

overall_design: Infection: Inoculated with H. pylori and treated with carcinogen ENNG (Treated) or control

first: Douglas

middle: S


title: Identification of Salmonella genes regulated by STM2239

status: Public on May 23 2013

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: Transcriptional profile of Salmonella enterica sv Typhimurium SL1344 ΔSTM2239 mutant cultures containing either a plasmid control (pFLAG-CTC) or a plasmid carrying STM2239 (pFLAG-STM2239) in the presence of IPTG.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Total RNA was harvested from three biological replicates of ΔSTM2239 mutant cultures with either a plasmid control (pFLAG-CTC) or a plasmid carrying STM2239 (pFLAG-STM2239) that were grown in LB to OD 0.5 with 1mM IPTG to induce plasmid-driven expression.

first: Steffen

last: Porwollik

last: Tomljenovic-Berube

first: Brian

last: Coombes


title: High risk HPV-positive lung carcinomas: molecular evidence for a pattern of pulmonary metastasis

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: BACKGROUND: Infection with high-risk types of human papillomavirus (hrHPV) is associated with cervical, anogenital and oropharyngeal cancers. A role for hrHPV in lung cancer has been proposed, although previous reports on the contribution of hrHPV infection to lung cancer have provided contradictory results. The current study evaluated hrHPV prevalence in lung tumor specimens of different histological subtypes in a Western study population using a validated test algorithm for hrHPV detection in formalin-fixed paraffin-embedded (FFPE) tumor specimen (i.e., GP5+6+-PCR and p16INK4A immunohistochemistry).   MATERIALS AND METHODS: Tumor tissue specimens from 228 lung cancer patients were subjected to GP5+6+-PCR and p16INK4A immunohistochemistry. hrHPV-positive tumors were further characterized using genotyping of GP5+/6+-PCR products, HPV E7 transcript analysis, loss of heterozygosity (LOH) analysis and array comparative genomic hybridization (arrayCGH), and the clinical history of patients was retrieved.   RESULTS: Three patients (3/228, 1.3%) with hrHPV-positive lung tumors were identified, revealing hrHPV types 16, 18 and 33, respectively. All three patients (1 male, 2 females) had a history of hrHPV-associated disease; two cervical carcinoma, and one oropharyngeal carcinoma. Further characterization revealed identical hrHPV genotype, pattern of p16INK4A expression, HPV E7 mRNA expression, and genomic aberrations in the individual pairings of lung tumor and foregoing hrHPV-associated cancer.    CONCLUSION: The present study found molecular evidence that supports association of  hrHPV in lung cancer with the presence of pulmonary metastasis of a hrHPV-positive cancer that originated elsewhere, and not with primary lung cancer in a Western population.

overall_design: 2 lung cancer samples (FFPE), 1 cervical cancer sample (FFPE), 1 head and neck cancer sample (FFPE)

first: Robert

last: Van Boerdonk

first: Johannes

last: Daniels

first: Oscar

last: Krijgsman

first: Elisabeth

last: Bloemena

first: Bauke

last: Ylstra

first: Peter

last: Snijders

first: Daniëlle

last: Heideman


title: Differential DNA methylation regions in cytokine and transcription factor genomic loci associate with childhood physical aggression

status: Public on May 22 2013

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

type: Methylation profiling by genome tiling array

summary: Animal and human studies suggest that inflammation is associated with behavioral disorders including aggression. We have recently shown that physical aggression of boys during childhood is strongly associated with reduced plasma levels of cytokines IL-1a, IL-4, IL-6, IL-8 and IL-10, later in early adulthood (Provencal et al., unpublished data). This study tests the hypothesis that there is an association between differential DNA methylation regions in cytokine genes in T cells and monocytes DNA in adult subjects and a trajectory of physical aggression from childhood to adolescence. We compared the methylation profiles of the entire genomic loci encompassing the IL-1a, IL-6, IL-4, IL10 and IL8 and three of their regulatory transcription factors (TF) NFkB1, NFAT5 and STAT6 genes in adult males on a chronic physical aggression trajectory (CPA) and males with the same background who followed a normal physical aggression trajectory (control group). We used the method of methylated DNA immunoprecipitation (MeDIP) with comprehensive cytokine gene loci and TF loci microarray hybridization, statistical analysis and false discovery rate correction.

overall_design: We recruited two groups of Caucasian males who were born in families with a low socioeconomic status and were living at the time of the present study within 200km from our laboratory. The first group, composed of 8 subjects, had a history of chronic physical aggression from age 6 to 15 years (chronic physical aggression group, CPA). The second group, composed of 12 subjects, was recruited from the same longitudinal studies but included only those who did not have a history of chronic physical aggression from age 6 to 15 (Control group, CG).  Using custom-designed microarrays with 44K probes tiling cytokines IL-1a, IL-6, IL-4, IL10 and IL8 and three of their regulatory transcription factors (TF) NFkB1, NFAT5 and STAT6, we obtained DNA methylation profiles by meDIP-chip.  Each profile was generated in triplicate.

first: Nadine

last: Provencal

first: Matthew

last: Suderman

first: Doretta

last: Caramaschi

first: Richard

last: Tremblay


title: Identification of genes essential for Moraxella catarrhalis growth under iron-limiting conditions using Genomic Array Footprinting (GAF): Expression analysis of directed gene deletion mutants.

first: Hester

last: Bootsma

summary: Iron-sequestration by the human host is a first line defense against respiratory pathogens like Moraxella catarrhalis, which consequently experiences a period of iron-starvation during colonization and infection. We determined the genetic requirements for M. catarrhalis growth during iron-starvation using the high-throughput genome-wide screening technology genomic array footprinting (GAF). To further characterize the functional consequences of the gene deletions (GAF identified genes), we determined transcriptome profiles of the wild-type and directed mutant strains during exponential growth in BHI medium.  The results described in this study are further discussed in Stefan P.W. de Vries, Peter Burghout, Jeroen D. Langereis, Aldert Zomer, Peter W.M. Hermans, Hester J. Bootsma: Genetic requirements for Moraxella catarrhalis growth under iron-limiting conditions, Molecular Microbiology.

overall_design: M. catarrhalis BBH18 directed mutants (n = 3) and their parental wild-type BBH18 strain (n = 4) were expanded to mid-log phase (OD620nm, 1.2 to 1.4) and RNA was isolated as previously described (de Vries et al., 2010 J Bacteriol 192: 3574-3583). Total RNA was labeled according to standard Nimblegen gene expression array protocols and hybridized to 4x72K custom design Nimblegen arrays for read-out.

first: Stefan

last: de Vries

last: Burghout

first: Jeroen

last: Langereis

first: Aldert

last: Zomer

last: Hermans


title: Real-time quantitative PCR analysis of microRNAs in human PBMC samples

status: Public on May 01 2013

city: Shenyang

first: zining

last: zhang

state: Liaoning

address: No 155, Nanjingbei street, Heping District

department: 1st affiliated hospital

institute: China Medical University

summary: A significant percentage of HIV-infected individuals experience a sharp decline in CD4+ T cell counts and progress to AIDS quickly after primary infection. Identification of biomarkers distinguishing rapid progressors (RPs) versus chronic progressors (CPs) is critical for early clinical intervention and could provide novel strategies to facilitate vaccine design and immune therapy. mRNA and miRNA expression profiles in the peripheral blood mononuclear cells (PBMCs) of RPs and CPs were investigated at 111±22 days (Mean±SD) of HIV infection. The association of mRNA and miRNA expression with disease progression was examined by receiver operating characteristic analysis and Kaplan-Meier survival analysis. Pathway enrichment analysis showed that genes with deregulated expression in RPs are primarily involved in apoptosis pathways. Furthermore, we found that 5 miRNAs (miR-31, -200c, -526a, -99a and -503) in RPs were significantly decreased compared to those in CPs (P<0.05). The decreased expression of these miRNAs was associated with rapid disease progression of HIV infection with a 94% predictive value as measured by the area under the curve. The upregulated predicted targets from the 5 signature miRNAs and all upregulated genes identified from mRNA microarray converged to the apoptosis pathway. Moreover, overexpression of miR-31 in primary human T cells promoted their survival. Our results have identified a distinct transcriptomic signature in PBMCs of RPs and provided novel insights to the pathogenesis of HIV infection.

overall_design: The initial 347 miRNA array was performed in 11 RPs, 6 CPs and 4 corresponding matched normal controls (training group); and only the miRNAs differentially expressed between RPs and CPs (P<0.05) in training group were detected in a subsequent validation group (19 RPs versus 10 CPs). miRNAs differentially expressed in 17 early HIV infected patients (including 11 RPs and 6 CPs) and 4 healthy controls in training cohort were firstly identified. Then, miRNAs differed RPs from CPs were compared in both training and validation cohort.

first: Zi-Ning

last: Zhang

first: Jun-Jie

last: Xu

first: Ya-Jing

last: Fu

first: You-Wen

last: He

first: Qi-Jing

last: Li

first: Hong

last: Shang


title: Systems Biology approach to identify transcriptome reprogramming in Arabidopsis thaliana during insect and bacterial attack (Pseudomonas syringae)

first: Per

last: Winge

overall_design: Arabidopsis thaliana (ecotype Colombia-0) seeds were sown into 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite). Plants were kept in growth chambers Vötsch VB 1514 (Vötch Industrietechnik GmbH, Germany) with a 8/16 h (light/dark) photoperiod at 22/18 °C, 40/70% relative humidity, and 70/0 mmol m-2 s-1 light intensity. The Pseudomonas syringae pv. tomato strain DC3000 culture was grown overnight in 10 ml of Kings B solution supplemented with antibiotics rifampicin (50 μg ml−1) and kanamycin (25 μg ml−1). Overnight culture was washed once in 10 mM MgCl2 and final cell densities were adjusted to approximately 0.20 at 600 nm (approximately 1.5 × 108 cfu ml−1) in 10 mM MgCl2. Plants were mock-challenged with 10 mM MgCl2 or inoculated with DC3000 strain, 3-4 leaves were infiltrated on the abaxial surface with a needleless 1-ml syringe.Whole rosettes were cut at the hypocotyls and harvested from Pseudomonas infested and mock-infected plants after 72 hours treatment. 4 biological replicates were prepared from each treatment, each containing rosettes from 15 individual plants. Differences in transcriptional responses were measured by comparing genes expression of Pseudomonas infected plants against mock-infected control plants.

first: Diem

middle: H

last: Tran

first: Torfinn

last: Sparstad

first: Pankaj

last: Barah

first: Atle

last: Bones


title: Microarray comparison of anterior and posterior Drosophila wing imaginal disc cells

status: Public on May 04 2013

city: Berlin

first: Ansgar

last: Klebes

address: Chausseestr. 117

department: Biology

institute: Humboldt University Berlin

summary:
Signaling between cells in the Anterior (A) and Posterior (P) compartments directs Drosophila wing disc development and is dependent on expression of the homeodomain transcription factor Engrailed (En) in P cells.  Downstream of en, posteriorly expressed Hedgehog (Hh) protein signals across the A/P border to establish a developmental organizer that directs pattern formation and growth throughout the wing primordium.  Here we extend investigations of the processes downstream of en by using expression array analysis to compare A and P cells.  102 candidate genes were identified that express differentially in the A and P compartments; four were characterized: Stubble (Sb) expression is restricted to A cells due to repression by en. CG15905, CG16884, and CG10200/hase und igel (hui) are expressed in A cells downstream of Hh signaling; and RNA interference for hui, Stubble, and CG16884 revealed that each is essential to wing development.
We carried out a global screen for genes with compartment-specific expression using expression array hybridization to compare transcript levels in A and P wing disc cells.

overall_design: GFP-labeled wing imaginal discs (ptc-Gal4/UAS-GFP and hh-Gal4/UAS-GFP) were micro-dissected  under a fluorescence dissecting microscope.  RNA isolation, amplification and microarray procedures were previously described (Klebes et al., 2002; Klebes et al., 2005; Klebes and Kornberg, 2008).   In brief, hybridization probes were generated by two rounds of T7-catalyzed linear RNA amplification and  labeled with Cy3 and Cy5 dyes. Reciprocally labeled probes (‘dye flip’) were hybridized to custom produced glass microarrays (GPL2581) that contained approximately 14,000 100-600 bp exon sequences that were generated by PCR.  Signal intensities were collected with a GenePix 4000B Scanner and processed with GenePix software (Molecular Devices) and global median normalized with NOMAD (http://ucsf-nomad.sourceforge.net/).

first: Thomas

last: Kornberg


title: Individual multidrug resistance patterns in AML patients point to the need for personalized molecular analysis

status: Public on May 31 2013

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

institute: University of Namur

summary:
In this unique study, based on paired samples obtained at AML diagnosis and at relapse, we assessed 380 multidrug-resistance-related genes, using TaqMan-based qRT-PCR,
as indicated by reports published over the past three decades.

overall_design: 11 paired AML samples taken at diagnosis and at relapse after treatment. Each patients act as its own control.

first: Chirayu

last: Patel

first: Jean-Pierre

last: Gillet

first: Leif

last: Stenke

first: Sudhir

last: Varma

first: Marita

last: Lindberg

first: Magnus

last: Björkholm

first: Jan

last: Sjöberg

first: Kristina

last: Viktorsson

first: Rolf

last: Lewensohn

first: Ola

last: Landgren

first: Michael

last: Gottesman


title: Transcription poisoning by topoisomerase I is controlled by gene length, splice sites and miR-142-3p

status: Public on Apr 17 2013

city: Fairfax

last: Ryan

state: VA

address: 11781 Lee Jackson Hwy, Ste 320

institute: In Silico Solutions

summary: DNA topoisomerase I (Top1) is required for transcription as it relaxes positive and negative supercoils by forming transient Top1 cleavage complexes (Top1cc) up- and down-stream of transcription complexes. However, Top1cc can also be trapped by endogenous DNA lesions and by camptothecin (CPT) and its anticancer derivatives, which results in transcription blocks. Here, we undertook a genome-wide analysis of the effects of CPT on gene expression at exon resolution.

overall_design: We tested the impact of Top1 inhibition on gene expression at the genome-wide level in human colon carcinoma HCT116 and human breast carcinoma MCF7 cells. The RNA of cells treated with camptothecin (CPT) for various times was analyzed with Affy Exon array (GeneChip Human Exon 1.0 ST array). Moreover, we tested the impact of Top1 down-regulation on gene expression at the genome-wide level in human colon carcinoma HCT116 cells. The RNA of cells treated transfected with a Top1 siRNA was analyzed with Affy Exon array (GeneChip Human Exon 1.0 ST array).

first: Stéphanie

last: Solier

first: Mike

middle: C

first: Kurt

last: Kohn

first: Hongfang

last: Liu

first: Barry

middle: R

last: Zeeberg

first: Yves

last: Pommier


title: Expression analysis of an amoxicillin resistant Escherichia coli strain

status: Public on May 27 2013

first: Nadine

last: Händel

address: Science Park 904

department: Swammerdam Institute for Life Sciences

institute: University of Amsterdam

summary:
Comparison of the whole genome gene expression level of an amoxicillin resistant E. coli strain with the wildtype it was derived from.
The process of amoxicillin adaptation of E. coli MG1655 wildtype cells is further descibed in van der Horst, M, J.M. Schuurmans, M. C. Smid, B. B. Koenders, and B. H. ter Kuile (2011) in Microb. Drug Resist. 17:141-147. Resistance to amoxicillin was induced in E. coli by growth in the presence of stepwise increasing antibiotic concentrations. To investigate consequences of the aquisition of amoxicillin resistance the transcriptomic profile of sensitive and resistant cells was compared in the absence and presence of sub-inhibitory (0.25xMIC) amoxicillin concentrations was compared.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Total RNA of 3 biological replicates of E. coli MG1655 wildtype cells and amoxicillin resistant cells cultured with (0.25xMIC) or without amoxicillin was hybridized on a 12x135k custom designed microarraychip against one common reference.

first: N

first: B

last: ter Kuile


title: Gene Expression of F. tularensis LVS in hepatocytic cell line FL83B vs LVS cultured in MH broth

status: Public on Jan 25 2013

city: Stony brook

first: Cindy

middle: A.

last: Thomas

state: New York

address: 280 CMM

department: Molecular Genetics and Microbiology

institute: Stony brook University

summary: Transcriptional profiling of LVS grown in hepatocytic cell line FL83B was compared to that of LVS cultued in MH broth to discover genes important for intracellular growth.

sample_organism: Francisella tularensis subsp. holarctica LVS

overall_design: Two-condition experiment, Intracellular  vs. Broth. Biological replicates: 4 Broth, 4 intracellular, independently grown and harvested. One replicate per array.

first: Huaixin

last: Zheng

first: Lance

last: Palmer

first: Martha

last: Furie


title: The expression profile of ABC transporter genes in post-treatment breast carcinomas

status: Public on Mar 01 2013

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

summary:
ATP-binding cassette (ABC) transporters contribute to development of resistance to anti-cancer drugs via ATP-dependent drug efflux. A major goal of our study was to investigate associations between expression of ABC transporters and outcome of breast carcinoma patients.
ABCA5/6/8/9/10, ABCB1/5/11, ABCC6/9, ABCD2/4 and ABCG5/G8 were significantly downregulated and ABCA2/3/7/12, ABCB2/3/8/9/10, ABCC1/4/5/10/11/12, ABCD1/3, ABCE1, ABCF1/2/3 and ABCG1 upregulated in post-treatment tumors compared with non-neoplastic tissues. Significant associations of ABCC1 and ABCC8 levels in tumors with grade and expression of hormonal receptors were found. ABCA13 and ABCD2 levels significantly associated with the response to neoadjuvant chemotherapy in post-treatment patients.

overall_design: Transcript levels of all forty nine human ABCs were determined by qPCR in post-treatment tumor and non-neoplastic tissue samples from 68 breast carcinoma patients treated by neoadjuvant chemotherapy. EIF2B1, MRPL19, IPO8, and UBB were used as reference genes for data normalization.

first: Viktor

last: Hlavac

first: Radka

last: Vaclavikova


title: Comparison between V. cholerae MO10 delta PTS mutant and wild type strain grown as planktonic or surface-associated cells

status: Public on Dec 10 2012

city: Boston

first: laetitia

last: Houot

address: 300 longwood av.

department: Infectious diseases

institute: children's Hospital Boston

summary: The PTS system is a central regulatory cascade in bacteria. Here, Vibrio cholerae PTS role was investagated during biofilm formation

overall_design: Analysis used wild type MO10 cells as control samples for comparison to the delta PTS strain. Strains were grown as planktonic (sample 1) or surface attached cells (sample 2). Experiment was done in triplicate with dye swap, which represent 6 independent microarray hybridizations.

first: Laetitia

first: Paula

last: Watnick


title: Deletion effect of HstD in gene expression

status: Public on Oct 17 2012

city: Higashihiroshima

first: Kazuhiro

last: Iwashita

state: Hiroshima

address: 3-7-1, Kagamiyama

institute: National Research Institute of Brewing

summary: In eukaryotic cells , histone deactylase plays key roles in the diverse process such as genomic stabillity, differenciation, and metabolism.  These enzymes also conserved in filamentous fungi, and their functios has been started to understand some fungal biological process such as development, stress responce, and secondary metabolism.  We found deletion of HstD  homolog of yeast Hst4, affected development, secondary metabolism in aspergillyus oryzae.  To acess the global effect of gene expression by HstD deletion, we performed microarray analysis, and results showed metabolite related gene was mainly alterd in DHstD.  This result sugested the HstD will concerned golobal regulation of secondary metabolism in filmatous fungi.

overall_design:
Control strain was used as refrence of dHstD strain. Two indipendent strain was used to this experiment.
biological replicate: Control-1, Control-2
biological replicate: dHstD-1, dHstD-2

first: Moriyuki

last: Kawauchi


title: Response of Porphyromonas gingivalis to nitrosative stress

status: Public on Oct 05 2012

city: Richmond

first: Janina

middle: P

last: Lewis

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

summary: Transcriptional profiling of P. gingivalis cells comparing cells grown in anaerobic conditions to cells grown in anaerobic conditions and exposed to nitrite and to GSNO.

overall_design: Two-condition experiment, anaerobically vs. anaerobically exposed to nitrosative stress cells. Biological replicates: 1 independently grown and harvested bacterial cells for each nitrosative exposure tested.  Four technical replicates for each experiment.

first: J


title: Expression data from Bifidobacterium animalis ssp. lactis strains exposed to hydrogen peroxide stress

status: Public on Feb 20 2013

city: Logan

first: Taylor

last: Oberg

state: UT

address: 8700 Old Main

department: NDFS

institute: Utah State University

summary:
Stress survival tactics in bacteria utilize the up- and down-regulation of stress response genes.  In bacteria that lack classical stress response genes for oxidative stress, other cellular systems can be used for cell survival.
We used custom microarrays to study the regulation of genes in Bifidobacterium animalis ssp. lactis strains to oxidative stress to elucidate novel stress response mechanisms.

sample_organism: Bifidobacterium animalis subsp. lactis DSM 10140

sample_organism: Bifidobacterium animalis subsp. lactis Bl-04

overall_design: Bifidobacterium cells were grown to late log phase then harvested and exposed to a sub-lethal level of hydrogen peroxide.  Samples were taken at 5 and 20 mins for RNA extraction and hybridization on Affymetrix microarrays. Controls were prepared for each time point which recieved no hydrogen peroxide treatment.

first: Jeff

last: Broadbent