title: Global gene expression profiling of Ehrlichia ruminantium virulent and attenuated strains

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: The obligate intracellular bacterium, Ehrlichia ruminantium (ER) is the causal agent of Heartwater, a fatal disease in ruminants. It is transmitted by ticks of the genus Amblyomma. Here, we report the genomic comparative and the global transcriptional profile of 4 strains of ER, Gardel and Senegal, two distant virulent strains with their corresponding attenuated strains. Our results showed a higher metabolic activity in attenuated strains compared to virulent strains, suggesting a better adaptation in vitro of attenuated strains to the host cells. There was a strong modification of membrane protein encoding genes expression for the 4 strains. A major over-expression of map1-related genes was observed for virulent strains, whereas attenuated strains over-expressed genes encoding for hypothetical membrane proteins. This result suggests that in vivo, MAP-1 related proteins could induce non-protective immune responses for virulent strains. For the attenuated strains, the lack of expression of map1-related genes and over-expression of other membrane proteins encoding genes could be important in induction of efficient immune responses.The diminution of expression of many genes in attenuated Senegal was caused by severe mutation. One of them, the gene recO is involved in DNA repair and its mutation could explain the higher proportion of mutated genes in attenuated Senegal, inducing the faster attenuation of Senegal compared to Gardel.

overall_design: Three biological replicates for each strain were used for the microarrays experiments and correspond to samples Gp38, Gp43, Gp44 (virulent gardel), Gp238, Gp243, Gp251 (attenuated Gardel), Sp7b, Sp8a, Sp8b (virulent Senegal) and Sp70, Sp75, Sp77 (attenuated Senegal). When 80% cell lysis was observed, samples containing supernatant and cellular debris were harvested and then ultra-centrifuged at 20 000 × g for 15 min at 4°C to collect elementary bodies (EB). Total RNA was extracted from the pellets using TRIzol reagent (Invitrogen). One color experiment with 4 experimental conditions (n=3) : virulent Gardel, attenuated Gardel, virulent Senegal, attenuated Senegal for a total of 12 samples.

first: N

last: Vachiery

first: P

last: Barbry

first: B

last: Mari

first: K


title: circular RNA profiling of LT-HSCs and MPPs

status: Public on May 01 2016

city: Beijing

first: Pengyan

last: Xia

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

country: China

institute: Institute of biophysics, Chinese Academy of Sciences

summary: Investigation of circular RNAs that have a higher expression level in LT-HSCs

overall_design: Arraystar Mouse circRNA Array analysis of circular RNA expression profiling using sorted LT-HSC and MPP samples from C57/BL6 strain. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols.

first: Shuo

last: Wang

first: Zusen

last: Fan


title: Transcriptome analysis of  non-human primate Chinese and Indian rhesus macaque spectrotype vaccination with Mycobacterium  bovis BCG

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary:
Global transcriptome analyses provide an excellent basis for the identification and definition of biomarkers with high relevance in infection processes, therapeutic intervention and protective immunity. The measurement applies three different state of the art transcriptomic technologies for global expression profiling to vaccine development. Different microarray platforms in conjunct to next generation sequencing (NGS) will build the basis for comparative approaches, such as up-down classification and correlation coefficients. This measurement is based on Agilent microarrays and a pre-clinical study with M. bovis BCG vaccination, using two different non-human primate Chinese and Indian rhesus macaque spectrotypes.
• Surrogate measurement using whole blood RNA
• 7 time points: d-14 and d0 (naïve, pre-immunization) and d1, d3, d7, d21, d42 post M. bovis BCG immunization
• Responses of two macaque spectrotypes
• Group size of 6 animals
European network of vaccine research and development (TRANSVAC)

overall_design: Microarray experiments were performed as single-color hybridizations using Agilent Technologies 4x44K Rhesus macaque gene expression microarrays

first: Frank

last: Verrek


title: Assessment of tumor heterogeneity, as evidenced by gene expression profiles, pathway activation, and gene copy number, in patients with multifocal invasive lobular breast tumors [gene copy number]

status: Public on Apr 30 2016

city: Jacksonville

first: Nadine

last: Norton

state: FL

address: 4500 San Pablo Road

department: Cancer Biology

country: USA

institute: Mayo Clinic

summary: Invasive lobular carcinoma (ILC) comprises approximately ~10-20% of breast cancers. In general, multifocal/multicentric (MF/MC) breast cancer has been associated with an increased rate of regional lymph node metastases. Tumor heterogeneity between foci represents a largely unstudied source of genomic variation in those rare patients with MF/MC ILC.

overall_design: We characterized gene copy number in 2 or more foci from 11 patients with MF/MC ILC (all ER+, HER2-) and adjacent normal tissue. RNA was extracted from 3x1.5mm cores from all foci. Gene copy number was measured using the Nanostring Cancer CNV panel, version 1. Copy number was compared between multiple foci within each patient.


title: Zebrafish 50% epiboly embryos: controls vs. Aplnra/b morphants

status: Public on Apr 29 2016

city: Toronto

first: Ian

middle: Cameron

last: Scott

state: Ontario

address: 686 Bay Street

department: Developmental and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Childen

summary:
Transcriptional profiling of 50% epiboly zebrafish embryos comparing wildtype (control) to Aplnra/b morpholino injected embryos.
Goal was to determine any gene expression changes in embryos deficient for the Apelin receptor.
Publication summary: The Apelin receptor (Aplnr) has been shown to be essential for proper cardiac progenitor migration during gastrulation. Loss of the Aplnr results in a delay in the ingression of lateral marginal cells and the complete absence of the heart and early cardiac gene expression.  How the Aplnr is required at a molecular level for cardiac progenitor migration remains completely unknown. We present evidence to suggest that the Aplnr enhances Nodal signaling to initiate the migration program at the correct time in development. Apelin receptor loss of function embryos exhibit a reduction in a wide range of Nodal target genes while activation of the receptor is capable of boosting their expression. Furthermore, Aplnr deficient embryos are exquisitely sensitive to Nodal receptor inhibitors. In order to directly interrogate the functional consequence of reduced Nodal signaling in the Aplnr cardiac phenotype, we raised the level of Nodal activity in aplnr mutants and found that this was able to provide a near complete rescue. We next sought to determine a mechanism by which lower Nodal signaling levels could translate into a delay in migration. Remarkably, we observe a delay in the expression of mesp family members in Aplnr loss of function embryos at the beginning of gastrulation. The mesp family has previously been implicated in mesodermal migration and we show that they are downstream targets of Nodal. We propose that in the absence of the Aplnr the appropriate Nodal threshold required to initiate the downstream cardiac progenitor “specification/migration” program requires a longer length of time to be attained. This translates into a delay in migration and consequently cardiac progenitors are not capable of reaching their final destination. In this study we demonstrate how the fine tuning of a key signaling pathway is critical for the proper development of the early embryo.

overall_design: Two-condition experiment, control vs. morphant: 4 Biological replicates

first: Ashish

middle: R

last: Deshwar

middle: C


title: Gene expression-based, individualized cancer progression outcome prediction for S61 stable transfectants

status: Public on Apr 26 2016

city: Taipei

first: Chen

middle: Shih

last: Wen

address: Changde St.

department: Graduate Institute of Oral Biology

country: Taiwan

institute: National Taiwan University

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling in stable transfectants

overall_design: To investigate whether knock-down s61 protein affect cancer progression

first: Shih-Wen

last: Chen

first: Chiang-Ting

last: Chou

first: Cheng-Chi

last: Chang

first: Yue-Ju

last: Li

first: Szu-Ta

first: I-Ching

last: Lin

first: Sang-Heng

last: Kokl

first: Shih-Jung

last: Cheng

first: Jang-Jaer

last: Lee

first: Tai-Sheng

last: Wu

first: Been-Ren


title: Assessment of tumor heterogeneity, as evidenced by gene expression profiles, pathway activation, and gene copy number, in patients with multifocal invasive lobular breast tumors [gene expression]

overall_design: We characterized gene expression and copy number in 2 or more foci from 11 patients with MF/MC ILC (all ER+, HER2-) and adjacent normal tissue. RNA was extracted from 3x1.5mm cores from all foci. Gene expression (730 genes) was measured using the Nanostring PanCancer Pathways Panel. Linear mixed models were employed to compare expression in tumor versus normal samples from the same patient, and to assess heterogeneity (variability) in expression among multiple ILC within an individual.


title: Assessment of tumor heterogeneity, as evidenced by gene expression profiles, pathway activation, and gene copy number, in patients with multifocal invasive lobular breast tumors

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: Expression data from MOLM-14 human acute myeloid leukemia cell line after AMPK activation by GSK621 according to mTORC1 activation level

status: Public on Apr 22 2016

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: AMPK activation by GSK621 induces cell death in acute myeloid leukemia. Surprisingly, we found that mTORC1 inhibition with rapamycin protects cells against GSK621-induced cytotoxicity. A genome-wide gene expression assay was performed to understand the molecular basis of this phenotype.

overall_design: MOLM-14 cells (biological replicates) were treated or not with rapamycin (10nM, 12h), then with an AMPK activator (GSK621, 30µM, 6h).

first: Pierre

last: Sujobert

first: Jérome

last: Tamburini


title: Analysis of microRNAs from exosomes in serum of  the mice, or in medium from in vitro differentiated mature brown fat cells

status: Public on Apr 15 2016

city: Bonn

first: Yong

address: Sigmund-Freud-Strasse 25

institute: University of Bonn

summary: We performed RT-PCR panels analysis of microRNAs expression in exosomes from the serum of wt mice, cold exposed mice or beta3 Adrenergic receptor agonist (CL-316.243) treated mice, and in exosomes from culture medium of mature brown adipocytes with or without cAMP treatment. Several microRNAs were identified as indicator correlated to brown adipocytes activity. The selected microRNAs may become potential biomarkers of brown fat activation in vivo

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: In vitro examination of exosomes from medium of mature brown adipocytes (BA-Exo; sample 1) and exosomes from medium of cAMP treated mature brown adipocytes (cAMP-BA-Exo; sample 2). In vivo examination of exosomes in serum from wild type mice (Serum-Exo#1 and Serum-Exo#2; sample 3 and sample 4), and serum from cold exposed mice (Cold-Serum-Exo#1 and Cold-Serum-Exo#2; sample 5 and sample 6), and serum from CL-316.243 treated mice (CL-Serum-Exo#1 and CL-Serum-Exo#2; sample 7 and sample 8)

first: Joschka

middle: J

last: Buyel

first: Franziska

last: Siegel

first: Joerg

last: Heeren

first: Alexander

last: Pfeifer


title: MicroRNA-122 Regulates Postnatal Polyploidization in the Murine Liver

status: Public on Mar 29 2016

city: Pittsburgh

first: Andrew

middle: W.

last: Duncan

state: PA

address: 450 Technology Drive, Suite 300

department: Pathology

institute: University of Pittsburgh

summary: A defining feature of the mammalian liver is polyploidy, a numerical change in the entire complement of chromosomes. The first step of polyploidization involves cell division with failed cytokinesis. Although polyploidy is common, affecting ~90% of hepatocytes in mice and 50% in humans, the specialized role played by polyploid cells in liver homeostasis and disease remains poorly understood. The goal of this study was to identify novel signals that regulate polyploidization, and we focused on microRNAs (miRNAs). First, to test whether miRNAs could regulate hepatic polyploidy we examined livers from Dicer1 liver-specific knockout mice, which are devoid of mature miRNAs. Loss of miRNAs resulted in a 3-fold reduction in binucleate hepatocytes, indicating that miRNAs regulate polyploidization. Secondly, we surveyed age-dependent expression of miRNAs in wild-type mice and identified a subset of miRNAs, including miR-122, that is differentially expressed at 2-3 weeks, a period when extensive polyploidization occurs. Next, we examined Mir122 knockout mice and observed profound, life-long depletion of polyploid hepatocytes, proving that miR-122 is required for complete hepatic polyploidization. Moreover, the polyploidy defect in Mir122 knockout mice was ameliorated by adenovirus-mediated over-expression of miR-122, underscoring the critical role miR-122 plays in polyploidization. Finally, we identified direct targets of miR-122 (Cux1, Rhoa, Iqgap1, Mapre1, Nedd4l and Slc25a34) that regulate cytokinesis. Inhibition of each target induced cytokinesis failure and promoted hepatic binucleation. Conclusion: Our data demonstrate that miR-122 is both necessary and sufficient in liver polyploidization. Among the different signals that have been associated with hepatic polyploidy, miR-122 is the first liver-specific signal identified. These studies will serve as the foundation for future work investigating miR-122 in liver maturation, homeostasis and disease.

overall_design: Livers from C57Bl/6 mice were isolated at defined ages: embryonic day 15.5 (n=3; mixed gender), 2 weeks (n=3; male), 3 weeks (n=3, male) and 7 weeks (n=3; male). Differential miRNA expression was assessed using the nCounter Mouse miRNA Expression Assay Kit (nanoString).

first: Shu-hao

last: Hsu

middle: W


title: Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation (expression)

status: Public on Apr 04 2016

city: Segrate

first: Luca

last: Petiti

state: Milan

address: Via Fratelli Cervi, 93

country: Italy

institute: ITB-CNR

summary: Gene expression profiling of  progenitor and differentiated keratinocytes by Affymetrix microarray

overall_design: Analysis of the transcriptome of progenitors and differentiated keratinocytes, in order to identify genes that are differentially expressed during human skin differentiation.

first: Alessia

last: Cavazza

first: Annarita

last: Miccio

first: Oriana

last: Romano

first: Guidantonio

middle: M

last: Tagliazucchi

first: Clelia

last: Peano

first: Marco

last: Severgnini

first: Ermanno

last: Rizzi

first: Gianluca

last: De Bellis

first: Silvio

last: Bicciato

first: Fulvio

last: Mavilio


title: E. coli MG1655 treated (G181D/R258C NusA) vs control (WT NusA) [II]

status: Public on Mar 28 2016

city: Hyderabad

first: M Zuhaib

last: Qayyum

state: Telangana

address: Lab of Transcription, CDFD,

country: India

institute: CDFD

summary: Transcription profiling of E. coli MG1655, representing the effect of G181D/R258C NusA in comparison to WT NusA

overall_design: Agilent one-color experiment,Organism: Escherichia coli ,Agilent Custom Ecoli Gene Expression Microarray 2x400k designed by Genotypic Technology Private Limited. (AMADID:72220)

first: Qayyum

last: M. Zuhaib

first: Dey

last: Debashish

first: Sen

last: Ranjan


title: E. coli MG1655 treated (G181D/R258C NusA) vs control (WT NusA) [I]

overall_design: Agilent one-color experiment,Organism: Escherichia coli ,Agilent Custom Escherichia coli Gene Expression Microarray 8x60K (AMADID: 48792) designed by Genotypic Technology Private Limited.     , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)


title: E. coli MG1655Δrac treated (N340S/G324D Rho) vs control (WT Rho)

summary: Transcription profiling of E. coli MG1655Δrac, comparing the effect Rho mutants (SBS: N340S, G324D) with WT Rho

overall_design: Organism: Escherichia coli ,Agilent Custom Escherichia coli Gene Expression Microarray 8x15K (AMADID: 020304) designed by Genotypic Technology Private Limited.

last: Zuhaib


title: E. coli MG1655 treated (BCM or WT rho) vs control (vector)

summary: Transcription profiling of E. coli MG1655 comparing the effect of Rho inhibitor: BCM

overall_design: Organism: Escherichia coli ,Agilent Custom Escherichia coli Gene Expression Microarray 8x15K (AMADID: 020304)designed by Genotypic Technology Private Limited.


title: Microarray to identify the differentially expressed genes in CFG treated SKOV3 cells compared with control cells under TGFbeta condition

status: Public on Mar 22 2016

city: Hangzhou

first: Fangfang

last: Tao

state: Zhejiang

address: 540 Binwen Road，binjiang district

institute: Zhejiang Chinese Medical University

summary: The compound fuling granule (CFG) is a traditional Chinese drug which has been used to treat ovarian cancer in China for over twenty years. Nevertheless, the underlying molecular mechanism of its anti-cancer effect remains unclear. In this study, microarray data analysis was performed to search for differentially expressed genes in CFG-treated ovarian cancer cells. Several cell cycle and epithelial-mesenchymal transition (EMT) related genes were identified. The microarray analyses also revealed that CFG potentially regulates EMT in ovarian cancer.

overall_design: 9 samples are analyzed, and 3 samples for each group,


title: Zygotes segregate entire parental genomes in distinct blastomere lineages causing cleavage stage chimaerism and mixolpoidy

status: Public on Mar 11 2016

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

type: Genome variation profiling by genome tiling array

summary: Chimaerism and mixoploidy define the presence of cell lineages with different parental genomes or different ploidy states in a single individual. Our knowledge on their mechanistic origin results from indirect observations, often when the cell lineages have been subject to rigorous selective pressure during development. Here, we applied haplarithmisis to infer the haplotypes and the copy number of parental genomes in 116 single blastomeres comprising entire preimplantation stage bovine embryos (n=23) following in vitro fertilization. Not only abnormal fertilizations leading to triploid zygotes, but also normally fertilized zygotes can spontaneously segregate entire parental genomes into different cell lineages during cleavage of the zygote. We coin the term “heterogoneic division” to indicate the events leading to non-canonical zygotic cytokinesis segregating the parental genomes into distinct lineages. Persistence of those cell lines during development is the likely cause of chimaerism and mixoploidy in mammals.

overall_design: Oocytes from eight Belgian Blue cows (Bos taurus) and semen from two Holstein-Friesian bulls (Bos taurus) were used for embryo production (BRP004 to BRP012 crosses). Eleven embryos were isolated at day-2  post insemination (pi) and 14 embryos were isolated on day-3 pi. Ovarian tissue from the donor cows (mothers) and semen from the two bulls (fathers) were used to extract bulk DNA (DNeasy Blood and Tissue kit, Qiagen). In addition, we obtained bulk DNA from the parents of the bulls (i.e. paternal grandparents of embryos). Moreover, DNA samples extracted from single blastomeres and the two expanded blastocysts (day-8 pi of BRP010 and BRP011 crosses) were whole genome amplified using the REPLI-g Single Cell Kit according to the manufacturer’s protocol (Qiagen). Subsequently, Single-cell and multi-cell parental or sibling DNA genotype calls, BAF and logR values were obtained from the BovineHD BeadChip raw intensity data by application of the GenCall algorithm, which is embedded in Illumina’s GenomeStudio software (http://illumina.com/software/genome_studio_software.ilmn). Genotypes were called by setting the GenCall score at 0.75 (based on the optimization steps described in Zamani Esteki et al. 2015). The raw LogR- and BAF-values as well as discrete SNP genotype calls were fed to a modified version of siCHILD algorithm (Zamani Esteki et al. 2015).

first: Aspasia

last: Destouni

first: Maaike

last: Catteeuw

first: Olga

last: Tšuiko

first: Eftychia

last: Dimitriadou

first: Katrien

last: Smits

first: Ants

last: Kurg

first: Andres

last: Salumets

first: Ann

last: Van Soom

first: Thierry

last: Voet

first: Joris

last: Vermeesch


title: Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance

status: Public on Mar 05 2016

city: Reno

first: Grant

last: Cramer

state: Nevada

address: 1664 N. Virginia St

department: Biochemistry & Molecular Biology

institute: University of Nevada, Reno

summary:
Background: Grapevine is a major food crop that is affected by global climate change. Consistent with field studies, dehydration assays of grapevine leaves can reveal valuable information of the plant’s response at physiological, transcript, and protein levels. There are well-known differences in grapevine rootstocks responses to dehydration. We used time-series transcriptomic approaches combined with network analyses to elucidate and identify important physiological processes and network hubs that respond to dehydration in three different grapevine species differing in their drought tolerance.
Results: Transcriptomic analyses of the leaves of Cabernet Sauvignon, Riparia Gloire, and Ramsey were evaluated at different times during a 24-h controlled dehydration. ANOVA revealed that 11,000 transcripts changed significantly with respect to the genotype x treatment interaction term and 6,000 transcripts changed significantly according to the genotype x treatment x time interaction term indicating massive differential changes in gene expression over time. Standard analyses determined substantial effects on the transcript abundance of genes involved in the metabolism and signaling of two known plant stress hormones, ABA and ethylene. ABA and ethylene signaling maps were constructed and revealed specific changes in transcript abundance that were associated with the known drought tolerance of the genotypes including genes such as VviABI5, VviABF2, VviACS2, and VviWRKY22. Weighted-gene coexpression network analysis (WGCNA) confirmed these results. In particular, WGCNA identified 30 different modules, some of which had highly enriched gene ontology categories for photosynthesis, phenylpropanoid metabolism, ABA and ethylene signaling. The ABA signaling transcription factors, VviABI5 and VviABF2, were highly connected hubs in two modules, one having overrepresentation in gaseous transport and the other in ethylene signaling. VviABI5 was distinctly correlated with an early response and high expression for the drought tolerant Ramsey and with little response from the drought sensitive Riparia Gloire. These ABA signaling transcription factors were highly connected to VviSNRK1 and other gene hubs associated with sugar, ethylene and ABA signaling. The ABA and ethylene signaling hubs were highly connected, supporting the hypothesis that there is substantial cross-talk between the two hormone pathways. This study identifies solid gene candidates for future investigations of drought tolerance in grapevine.

sample_organism:
Vitis vinifera
Vitis riparia
Vitis x champinii

overall_design: Fully mature Cabernet Sauvignon, Riparia Gloire, and Ramsey leaves were dehydrated (Hopper et al., 2014) to assess rapid transcriptomic changes. Briefly, the leaf was excised from the plant and placed into a dehydration box for various time points over a 24-h period. Leaf dehydration occurred in the air above a solution of 333 mM NaCl in a sealed container in a growth chamber. Leaves were removed from the box and immediately frozen in liquid nitrogen. Control samples were taken from the same plant at the corresponding time to account for any circadian effect on transcript abundance. RNA was extracted from three experimental replicates for treatment and control samples at each time point.

first: Daniel

last: Hopper

first: Ryan

last: Ghan

first: Karen

middle: A

last: Schlauch


title: Gene expression profile of LAPC4 stimulated by 5α-Abi

status: Public on Mar 01 2016

city: Cleveland

first: Nima

last: Sharifi

state: OH

address: 9500 Euclid ave

department: Cancer biology

institute: Cleveland CLinic

summary: LAPC4 cells were starved for 2 days and stimulated with 1µM 5α-Abi or 0.1nM DHT. Gene expression profiles are detected to determine the effect of 5a-Abi on prostate cancer cell line.

overall_design: LAPC4 cells were starved for 2 days with phenol red-free and serum free-medium  and stimulated with 1µM 5α-Abi or 0.1nM DHT for 48h. Gene expression profiles are detected to determine the effect of 5a-Abi on prostate cancer cell line.

first: Zhenfei

last: Li


title: Genetical genomics implicates the IAA biosynthesis pathway in the regulation of Populus adventitious root formation

city: Gainesville

first: Christopher

last: Dervinis

address: 2033 Mowry Road, rm 320

department: SFRC

institute: University of Florida

summary: Adventitious roots (AR) develop from tissues other than the primary root, in a developmental process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of several crops. Here we quantified the number of AR, root architectural traits and root biomass in cuttings from a pseudo-backcross population of Populus deltoides and Populus trichocarpa. Quantitative trait loci (QTL) mapping and whole-transcriptome analysis of individuals carrying alternative QTL alleles for AR number wereas used to identify putative regulatorsregions in the genome that regulateof AR development in the genome., and putative candidate genesregulators.

overall_design:
Gene expression in three individuals carrying alleles that originated from the P. trichocarpa grandparent (UF352, UF498 and UF926, referred hereafter as the PtQTL genotype category) was contrasted with those with alleles from the P. deltoides grandparent (UF717, UF209 and UF912, or the PdQTL genotype category).  25 cuttings of each of the six selected genotypes (3 PtQTL and 3 PdQTL)  were grown in hydroponic solution, and basal (1 cm) cutting sections from four biological replicates of each genotype were collected at each of five time points (0, 24, 48, 96 and 192 hours after cuttings were harvested). Total RNA was extracted from the bottom 1 cm stem section collected from each sample. The sample included xylem, phloem and bark. RNA was purified using RNeasy Mini Kit columns (Qiagen), and DNase treated with RNase-Free DNase set (Qiagen). RNA quality was evaluated in 1% w/v agarose gels. RNA was amplified and cRNA synthesized and labeled using Two Dyes Agilent Low Input Quick Amp Labeling Kit (Agilent). The microarray platform used consisted of single 60-mer probes designed for each of 43,803 predicted gene models from the sequenced genome of P. trichocarpa version 2. These probes were previously selected for being suitable for analysis of gene expression in this mapping population.
A total of 60 microarrays were used in the transcriptome analysis and each microarray was hybridized with 2 samples labeled with Cy3 or Cy5. Gene expression of each of six genotypes was analyzed in five time points (0, 24, 48, 96 and 192 hours), with four biological replicates per genotype and time point, following a “bird cage” design . The design was selected to favor contrasting gene expression of samples from different QTL categories (PtQTL and PdQTL) at each time point, as well as samples from the same genotype, collected from different time points. Median values of signal intensities were quantile normalized and log2 transformed. Normalized signals were analyzed in SAS 9.2 (SAS Institute Inc. 9.2® 2004, Cary, NC, USA) using a mixed-model ANOVA with genotype and genotype × time interactions as fixed effects, and microarray as random effect. Differences in expression between the group of genotypes from the PtQTL and PdQTL categories were estimated at each time point, and the significance was determined based on a false discovery rate (FDR) of 5%

first: Cintia

middle: L

last: Ribeiro

first: Cynthia

last: Silva

first: Derek

last: Drost

first: Evandro

last: Novaes

first: Carolina

first: Matias

last: Kirst


title: Environmental enteric dysfunction includes a broad spectrum of inflammatory responses and epithelial repair processes (RT-PCR)

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Environmental enteric dysfunction (EED), a chronic diffuse inflammation of the small intestine, is associated with stunting in children in the developing world. The pathobiology of EED is poorly understood because of the lack of a method to elucidate the host response. This study utilized a novel microarray method to interrogate the host transcriptome in feces in Malawian children with EED.  Our data showed that the children studied had a range of %L values, consistent a spectrum of EED from normal to severe. We identified 12 transcripts associated with the severity of EED, including chemokines that stimulate T-cell proliferation, Fc fragments of multiple immunoglobulin families, interferon-induced proteins, activators of neutrophils and B-cells, and mediators that dampen cellular responses to hormones. EED associated transcripts mapped to pathways related to cell adhesion, and responses to a broad spectrum of viral, bacterial and parasitic microbes and enhanced phagocytosis. Several mucins, regulatory factors and protein kinases associated with the maintenance of the mucous layer were expressed less in children with EED than normal children.  In conclusion, EED represents the focused activation of elements of the immune system and is associated with widespread intestinal barrier disruption. The differentially expressed transcripts may be explored as potential biomarkers.

overall_design: This study was carried out, firstly using Affymetrix Human Transcriptome Array 2.0 (HTA2.0, data have already been deposited in the GEO database: GSE74681) to profile the transcriptome of the host stool RNAs in 259 subjects, and then using droplet digital PCR (ddPCR) assays to validate the microarray data in terms of signal correlation. The ddPCR assay was done for a total of 60 genes in 25 - 236 (median 67) of the 258 RNA samples per RNA availability (1 of 259 samples [stool_080B] was not used for any of the 60 assays due to lack of availability). The data of the first 42 assays (genes) in the matrix sheets were used in Figure 4 for signal correlation analysis, and the data of the rest 18 assays (genes) were used in Table 4 for validation of 18 significant genes identified in biological pathway analysis.

first: Jennifer

last: Stauber

first: Nurmohammad

last: Shaikh

first: Isabel

last: Ordiz

first: Mark

last: Manary


title: Confounding factors in the analysis of the transcriptome response to UV exposure in skin of wild-type and human p53-variant mice

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

institute: University of Amsterdam

summary:
An in-vivo experiment with UV-B exposure of the skin of nude, male mice, with and without human-derived p53 variants in their genome to investigate the cellular responses upon UV-induced DNA damage.
Essentially, 4 replicate mice were used for each level of UV-exposure. For each mouse a biopsy of the skin was sampled 5-6 times at different recovery time points after UV-pulse exposure, which resulted in paired samples. In total 132 treated and 132 untreated samples were taken from 64 male mice.

overall_design: 264 skin biopsies were taken from 48 mice on 10 timepionts and for 3 different UV-B doses. 3 different genotypes of mice were used, Wild-type (WT; p53+/+), p5372R/72R, and p5372P/72P.  Later, it was determined that eight samples came from female mice instead of male mice.  Therefore, the eight samples were excluded further analyses (no processed data were generated from these arrays).

first: Wendy

last: Rodenburg

first: Conny

last: van Oostrum

first: Paul

middle: F

last: Wackers

first: Martijs

last: Jonker

first: Rob

last: Dekker

first: Han

last: Rauwerda

first: Wim

last: Ensink

first: Annemieke

last: de Vries

first: Timo

last: Breit


title: Abscisic Acid Transcriptomic Signaling Varies with Grapevine Organ

first: Grant

last: Cramer

summary:
Background: Abscisic acid (ABA) regulates various developmental processes and stress responses over both short (i.e. hours or days) and longer (i.e. months or seasons) time frames. To elucidate the transcriptional regulation of early responses of grapevine (Vitis vinifera) responding to ABA, different organs of grape (berries, shoot tips, leaves, roots and cell cultures) were treated with 10 μM (S)-(+)-ABA for 2 h. NimbleGen whole genome microarrays of Vitis vinifera were used to determine the effects of ABA on organ-specific mRNA expression patterns.
Results: Transcriptomic analysis revealed 839 genes whose transcript abundances varied significantly in a specific organ in response to ABA treatment.  No single gene exhibited the same changes in transcript abundance across all organs in response to ABA. The biochemical pathways affected by ABA were identified using the Cytoscape program with the BiNGO plug-in software. The results indicated that these 839 genes were involved in several biological processes such as flavonoid metabolism, response to reactive oxygen species, response to light, and response to temperature stimulus. ABA affected ion and water transporters, particularly in the root. The protein amino acid phosphorylation process was significantly overrepresented in shoot tips and roots treated with ABA. ABA affected mRNA abundance of genes (CYP707As, UGTs, and PP2Cs) associated with ABA degradation, conjugation, and the ABA signaling pathway. ABA also significantly affected the expression of several transcription factors (e.g. AP2/ERF, MYC/MYB, and bZIP/AREB). The greatest number of significantly differentially expressed genes was observed in the roots followed by cell cultures, leaves, berries, and shoot tips, respectively. Each organ had a unique set of gene responses to ABA.
Conclusions: This study examined the short-term effects of ABA on different organs of grapevine. The responses of each organ were unique indicating that ABA signaling varies with the organ. Understanding the ABA responses in an organ-specific manner is crucial to fully understand hormone action and plant responses to water deficit.

overall_design: Shoot tips and berries samples were collected at the University of California, Davis, CA, USA (2010); cell culture samples were sampled at Oregon State University, OR, USA (2010); roots and leaf samples were collected at the University of Nevada, Reno, Reno, NV, USA (2011). Three independent experimental (and biological) replicates were harvested to compare between ABA-treated and untreated samples. Tissue was derived from Vitis vinifera L. cv. Cabernet Sauvignon.

first: Supakan

last: Rattanakon

first: Ryan

last: Ghan

first: Gregory

last: Gambetta

first: Laurent

middle: G

last: Deluc

first: Karen

last: Schlauch


title: Integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell carcinoma

status: Public on Feb 29 2016

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

summary: Genomic instability plays an important role in human cancers.  We previously characterized genomic instability in esophageal squamous cell carcinomas (ESCC) in terms of loss of heterozygosity (LOH) and copy number (CN) changes in tumors. In the current study we focus on biallelic loss and its relation to expression of mRNA and miRNA in ESCC using results from 500K SNP, mRNA, and miRNA arrays in 30 cases from a high-risk region of China.

overall_design: 30 matched tumors and normal tissue

last: Hu

first: Philip

last: Taylor

middle: H


title: miRNA expression changes in small intestinal lamina propria leukocyte samples during the course of SIV infection of rhesus macaques

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: This study describes differential miRNA expression in small intestinal lamina propria leukocyte samples longitudinally during the course of SIV infection of rhesus macaques. Notably, the T-cell activation associated miR-15b, miR-142-3p, miR-142-5p and miR-150 expression was significantly downregulated at 90 and 180DPI. Further, reporter and overexpression assays validated IRAK1 as a direct miR-150 target. Furthermore, IRAK1 protein levels were markedly elevated in intestinal LPLs and epithelium. Finally, blockade of CD8+ T-cell activation/proliferation with delta-9 tetrahydrocannabinol (9-THC) significantly prevented miR-150 downregulation and IRAK1 upregulation. Our findings suggest that miR-150 downregulation during T-cell activation may disrupt the translational control of IRAK1 facilitating persistent GI inflammation.

overall_design: We performed TaqMan Low Density Array based high throughput miRNA analysis longitudinally on intestinal lamina propria cells isolated before and thereafter at 21, 90 and 180 days post intravenous inoculation of rhesus macaques with 100TCID50 of SIV. microRNA reverse transcription and preamplification was performed according to the manufacturer’s recommendation. Data analysis was performed using RQ Manager 1.2.2 and DataAssist v3.01 software. Data was normalized to two endogenous controls, namely, snoU6 and RNU48. Due to the small sample size and exploratory nature of the study, multiple comparisons correction was not performed.

first: M


title: Protoarray based identificatoin of dysregulated proteins in metastatic osteosarcoma

status: Public on Feb 24 2016

city: Houston

first: Tsz-Kwong

last: Man

state: TX

address: 1102 Bates,

department: Pediatrics

institute: Baylor College of Medicine

summary:
Our results successfully showed through profiling of 8268 proteins that five autoantibodies in the metastatic group showed significantly higher intensities than non-metastatic and control groups
Healthy or non-cancerous pediatric patients were pooled into a control group; Human ProtoArray that contains total 19200 protein spots of which 1326 are control spots and  8,268 are unique human proteins

overall_design: In the study presented here we pooled plasma samples from Osteosarcoma patients who developed metastasis and localized disease within the first year of follow-up into a metastatic group and a non-metastatic group respectively and were used to acquire expression profiles of a total of 8268 proteins leading to successful identification of 5 proteins.

first: Manjula

last: Nakka


title: Pollutants bioavailability and toxicological risk from NSAIDs to marine mussels

status: Public on Feb 22 2016

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

institute: University of Padova

summary: Pharmaceutical compounds are emerging contaminants in aquatic environment due to their massive use (human and veterinary medicines, agriculture and aquaculture) and a limited removal by waste water treatment plants (WWTPs).  In this work, a representative determination of ecotoxicological potential of two different NSAIDs compounds was studied in the sensitive bioindicator marine organism M. Galloprovincialis. Mussels were exposed, under regulated laboratory conditions, to Ketoprofen (KET) and Nimesulide (NIM), dosed alone at the realistic environmental concentration of 0.5µg/L for 14 days. Gene expression analyses of Mytilus galloprovincialis exposed to KET and NIM  have been performed through a DNA microarray platform.

overall_design: Mussels Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater, at 18  ± 1 °C, 37 ‰ salinity, pH 7.5 ± 0.5 and oxygen saturation >94%. Mussels were distributed into three 17 L aquarium and exposed at 0.5µg/L to ketoprofen (KET) and nimesulide (NIM) dosed alone for 14 days. All treatments were compared to control (CTRL) containing 0.00001% of methanol. Water was changed every other day and concentration of molecules were restored. Gene transcription analyses of 12 digestive glands pools (four pools for each treatment composed by 3 digestive glands; CNTR, NIM and KET) were performed using a 8X60K Agilent oligo-DNA microarray platform GPL18667. Microarrays were synthesized in situ using the Agilent non-contact ink-jet technology including default positive and negative controls. Total RNA was isolated using Extract-all (Eurobio) procedure. RNA quality and integrity was controlled on the Agilent bioanalyzer using RNA nanochips and Agilent RNA 6000 nanoreagents (Agilent Technologies, Waldbronn, Germany). RNA concentrations were measured at 260 nm using a ND-1000 spectrophotometer (Nanodrop Technologies) using the conversion factor 1 OD = 40 mg/mL total RNA. Samples were stored at -80°C until further use. Gene expression profiling was performed using an Mytilus galloprovincialis oligo-DNA microarray of 59,971 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA at a resolution of 2 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. FeatureExtraction v10.7.3.1 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Luca

last: Bargelloni

first: Marica

last: Mezzelani

first: Francesco

last: Regoli


title: Validation of a genome-wide search for zebra finch epigenetically regulated genes using Zebra finch Exon Arrays

city: Seewiesen-Starnberg

first: Carolina

last: Frankl-Vilches

state: Bavaria

address: Eberhard-Gwinner-Str. 6a

department: Behavioural Neurobiology

institute: Max Planck Institute for Ornithology

summary: DNA methylation is tightly linked with gene expression regulation and has long been regarded a stable epigenetic mark in postmitotic cells. However, it recently became clear that postnatal brains appear to show stimulus-induced de novo CpG methylation or active demethylation related to neuronal plasticity. Due to striking homologies between the brains of birds and mammals, songbirds, especially the zebra finch, propose an attractive model for investigating the genome-wide DNA methylation profile and DNA methylation reconfiguration during brain development. In order to obtain a first genome-wide compendium of genes under putative DNA methylation control, we performed MethyCap-seq experiments on two recently cultured zebra finch cell lines, G266 and ZFTMA, also upon AZA-induced demethylation. First, the MethylCap-seq methodology in zebra finch was validated by comparison with RRBS generated data. Subsequently, quantitative analysis identified 30,700 significantly demethylated loci upon AZA-treatment. Further examination revealed enrichment of these regions in exons and promoters. To assess the influence of methylation on gene expression, RNA-seq experiments were performed. Comparison of the RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed obvious enrichment for neurological networks. The ZF exon-arrays analysis validated the RNA-seq expression result for 75% and 62%, of the down and up-regulated genes, respectively. A subset of genes was validated also using qPCR and CpG pyrosequencing. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control

overall_design:
Within the overall project, we performed a set of microarrays to validate RNAseq data (Series accession number GSE61060) . DMSO- and AZA-treated zebra finch cell lines, i.e. G266 and ZFTMA.
ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided for individual Sample records. Processed data is available on Series record.

first: C

first: A

last: Bakker

first: J

last: Diddens

first: N

last: Sohnius


title: Nimblegen microarrays gene expression analysis of porcine transformed MSCs and sarcomas

status: Public on Feb 23 2016

city: Basel

first: Morgane

last: Ravon

address: Grenzacherstrasse

country: Switzerland

institute: Hoffman-La Roche

summary: Osteosarcoma is a relatively rare solid tumour, but the most common primary bone cancer. It predominantly affects young people and is highly malignant, requiring aggressive surgical resection and cytotoxic chemotherapy. Five-year survival for patients with metastatic osteosarcoma is only around 30% 14. We report that pigs with heterozygous and homozygous inactivation of TP53 consistently develop osteosarcomas, providing a new model of osteosarcoma at human scale to understand and treat this devastating disease. Gene expression profiling and data analysis was further described in 'A porcine model of osteosarcoma' by Anja Saalfrank et al. (2016).

overall_design: Differential gene expression profiles of MSCs and sarcomas relative to wild type in order to identify transcriptional changes associated with the stages of porcine MSC transformation

first: Ulrich

last: Certa


title: Comparison of overall functional gene structures of a membrane bioreactor (MBR) and an oxidation ditch (OD) running parallelly at full-scale

city: Beijing

first: Yu

last: Xia

state: Beijing

address: Tsinghua University, Haidian District

department: Environmental school

institute: Tsinghua Univeristy

summary: Membrane bioreactor (MBR) systems are typically known different from conventional activated sludge (CAS) systems in operational parameters, while current knowledge of their microbial differentiations is barely sufficient. To this end, the current study was launched to address the differences of the overall functional genes of an oxidation ditch (OD) and an MBR running parallelly at full-scale using a functional gene array-GeoChip 4.2.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Two full-scale wastewater treatment systems applying the processes of oxidation ditch (OD) and membrane bioreactor (MBR) were investigated. They treated identical wastewater at the same scale. 12 mixed-liquor suspended sludge (MLSS) samples collected daily on 12 consecutive days from each system were analyzed by GeoChip 4.2.

first: Xianghua

last: Wen


title: Genome-wide profiling of copy-number alteration in monoclonal gammopathy of undetermined significance

status: Public on Feb 18 2016

city: Newcastle upon Tyne

first: Aneta

last: Mikulasova

address: Brewery Lane

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

summary: Monoclonal gammopathy of undetermined significance (MGUS) is a benign condition with an approximate 1% annual risk of symptomatic plasma cell disorder development, mostly to multiple myeloma (MM). We performed genome-wide screening of copy-number alterations (CNAs) in 90 MGUS and 33 MM patients using high-density DNA microarrays. We identified CNAs in a smaller proportion of MGUS (65.6%) than in MM (100.0%, p=1.31×10-5) and showed median number of CNAs is lower in MGUS (3, range 0-22) than in MM (13, range 4-38, p=1.82×10-10). In the MGUS cohort, the most frequent losses were located at 1p (5.6%), 6q (6.7%), 13q (30.0%), 14q (14.4%), 16q (8.9%), 21q (5.6%) and gains at 1q (23.3%), 2p (6.7%), 6p (13.3%) and Xq (7.8%). Hyperdiploidy was detected in 38.9% of MGUS cases and the most frequent whole chromosome gains were 3 (25.6%), 5 (23.3%), 9 (37.8%), 15 (23.3%) and 19 (32.2%). We also identified CNAs such as 1p, 6q, 8p, 12p, 13q, 16q losses, 1q gain and hypodiploidy, which are potentially associated with an adverse prognosis in MGUS. In summary, we showed that MGUS is similar to MM in that it is a genetically heterogeneous disorder, but overall cytogenetic instability is lower than in MM, which confirms that genetic abnormalities play important role in monoclonal gammopathies.

overall_design: A total of 90 patients with monoclonal gammopathy of undetermined significance and 33 patients with multiple myeloma were included in this study. An abnormal plasma cell population (CD138+CD19-CD56+/-) was isolated from all MGUS patients and one MM patient. A normal plasma cell population (CD138+CD19+CD56-) was also isolated from 13 out of 90 MGUS patients. In the remaining 32 MM samples, CD138+ plasma cells were obtained. Promega Human Genomic DNA or Agilent Human Reference DNA was used as reference DNA.

first: Jan

last: Smetana

first: Marketa

last: Wayhelova

first: Helena

last: Janyskova

first: Viera

last: Sandecka

first: Zuzana

last: Kufova

first: Martina

last: Almasi

first: Jiri

last: Jarkovsky

first: Evzen

last: Gregora

first: Petr

last: Kessler

first: Marek

last: Wrobel

first: Brian

last: Walker

first: Christopher

middle: P

last: Wardell

first: Gareth

last: Morgan

first: Roman

last: Hajek

last: Kuglik


title: Identification of the genetic loci associating with the OMV formation by means of transcriptome analysis on the isogenic BF2766 mutants in B. fragilis strain YCH46

status: Public on Feb 21 2016

city: Kagawa

first: Imaohji

last: Haruyuki

department: Medicine

country: Japan

institute: Kagawa University

summary: The human gut microbe Bacteroides fragilis can alter the expression of its surface molecules such as capsular polysaccharides and SusC/SusD family outer membrane proteins through the reversible DNA inversions.　We have revealed that the outer membrane vesicle (OMV) formation in B. fragilis is regulated by BF2766 (tyrosine recombinase)-mediated DNA inversions at two distantly located promoter regions previously designated as class IV regions. In this study, we aimed to identify the genetic loci associating with the OMV formation by means of transcriptome analysis on the isogenic BF2766 mutants. By comparing the transciptomes of four BF2766 deletion mutants, in which the promoter orientations in class IV-1 and IV-2 regions were locked ON/ON, OFF/ON, OFF/OFF, or ON/OFF, we found that the transcription of the genes downstream of class IV-2 markedly elevated in a hyper-vesiculating ON/ON strain.

overall_design: A four chip study using total RNA isolated from four BF2766 deletion mutants culture. Each sample contains duplicated data.

first: Haruyuki

last: Nakayama-Imaohji

first: Tomomi

last: Kuwahara


title: Murine BCC Cells: dio3 interfered vs control

city: Naples

first: Monica

last: Dentice

address: Via S. Pansini 5

department: Department of Clinical Medicine and Surgery

institute: University of Naples "Federico II"

summary: MicroRNA expression profiling of mouse basal cell carcinoma (BCC) cells comparing BCC cells transfected with a stealth for dio3 transcript or control stealth-RNA.

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

overall_design: Two-condition experiment, Stealth-D3 vs Stealth-CTR cells. Biological replicates: 3 Stealth-D3 and 3 Stealth-CTR, independently grown and harvested. Single RNA were pooled. One replicate per array.

first: Raffaele

last: Ambrosio

first: Domenico

last: Salvatore


title: Specific IMPC gene expression signature

status: Public on Feb 26 2016

city: Paris

first: Nadège

last: GRUEL

address: 26 rue d'Ulm

department: Translational Research and U830 INSERM Unit

institute: Institut Curie

summary:
Polarity defects are a hallmark of most carcinomas. Cells from invasive micropapillary carcinomas (IMPCs) of the breast are characterized by a striking cell polarity inversion and represent a good model for the analysis of polarity abnormalities. We have performed an in-depth investigation of polarity alterations in 24 IMPCs, compared with invasive carcinomas of no special type (ICNST).
We used microarrays to compared gene expression profilings of IMPC with ICNST in a training set and in validation one.

overall_design: 124 breast cancer samples: 73 IMPC and 51 ICNST (training set: 63 samples and validation set: 61 samples)

last: Gruel

first: Anne

last: Vincent-Salomon


title: Functional gene diversity of microbial communities sampled in 2010 in CiPHER site, Aklaska

city: Norman

first: Jizhong

last: Zhou

state: OK

address: 101 David L Boren Blvd

department: Department of Microbiology and Plant Biology

institute: University of Oklahoma

summary: The response of soil microbial community to climate warming through both function shift and composition reorganization may profoundly influence global nutrient cycles, leading to potential significant carbon release from the terrain to the atmosphere. Despite the observed carbon flux change in northern permafrost, it remains unclear how soil microbial community contributes to this ecosystem alteration. Here, we applied microarray-based GeoChip 4.0 to investigate the functional and compositional response of subsurface (15~25cm) soil microbial community under about one year’s artificial heating (+2°C) in the Carbon in Permafrost Experimental Heating Research site on Alaska’s moist acidic tundra. Statistical analyses of GeoChip signal intensities showed significant microbial function shift in AK samples. Detrended correspondence analysis and dissimilarity tests (MRPP and ANOSIM) indicated significant functional structure difference between the warmed and the control communities. ANOVA revealed that 60% of the 70 detected individual genes in carbon, nitrogen, phosphorous and sulfur cyclings were substantially increased (p<0.05) by heating. 18 out of 33 detected carbon degradation genes were more abundant in warming samples in AK site, regardless of the discrepancy of labile or recalcitrant C, indicating a high temperature sensitivity of carbon degradation genes in rich carbon pool environment. These results demonstrated a rapid response of northern permafrost soil microbial community to warming. Considering the large carbon storage in northern permafrost region, microbial activity in this region may cause dramatic positive feedback to climate change, which is important and necessary to be integrated into climate change models.

sample_organism:
Bacteria
Archaea
Eukaryota
Viruses
synthetic construct

overall_design:
A total of 12 soil samples were analyzed for functional genes of microbial communities. The soil samples include soil warming treatment and control with six biological replicates.
Please note that the *532.exp.ftr files recorded intensities of targeted spots, and *532.void.ftr files were intensities of the areas between two adjacent targeted spots, which were used as background intensity (noise) in the normalization step in GeoChip.

first: Mengting

last: Yuan

first: Kai

last: Xue

first: Lei

last: Cheng

first: Zhou

last: Shi

first: Ye

last: Deng

first: Joy

last: Van Nostrand

first: Zhili

last: He

first: Liyou

last: Wu


title: Emergence of cephalosporin resitance in cephalosporin-sensitive class A penicillin binding protein mutants in Enterococcus faecium

status: Public on Feb 19 2016

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
E. faecium is inherantly resistant to cephalosporins.  Resistance is lost in Class A penicillin binding protein PbfF PonA mutants, but is reversible by pencillin exposure.
E. faecium Affymetrix GeneChips were used to compare E. faecium expression properties of pbfF ponA mutant cells in the absence or presence of penicillin exposure.
Significant differences were observed between the expression properties of mock and penicillin treated E. faecium CV571 (pbfF ponA double mutant) cells.

overall_design: E. faecium strain CV571 (pbfF ponA) were grown in laboratory medium to exponential under aerobic growth conditions.  Cells were either mock treated or treated with penicillin for 30 min, total bacterial RNA was isolated, labeled and applied to Affymetrix GeneChips.  We sought to determine whether the transcriptional profiles of E. faecium pbfF ponA mutant cells of penicillin challenged cells differed from that of mock treated CV571 cells.

first: Louis

last: Rice


title: Fibroblast growth factor 9 inhibits remyelination via an off target effect on astrocytes in multiple sclerosis

status: Public on Feb 17 2016

city: Glasgow

first: Manikhandan

middle: A V

last: Mudaliar

state: Scotland

address: Room B528, Sir Graeme Davies Building, 120 University Place

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

summary:
Failure of remyelination in multiple sclerosis (MS) is associated with inhibition of oligodendrocyte precursor (OPC) differentiation, but the cellular and molecular mechanisms involved remain poorly understood. We now report inflammatory demyelination in MS is associated with localized expression of fibroblast growth factor 9 (FGF9) by oligodendrocytes and to a lesser extent astrocytes, and demonstrate FGF9 inhibits myelination and remyelination in vitro. This inhibitory activity is reversible and due to an off target FGF9-dependent effect on astrocytes that disrupts in the growth factor milieu required to support myelination.

We identify multiple downstream events induced by FGF9 associated with this effect including increased expression of leukaemia inhibitory growth factor (LIF) and FGF2, both of which are shown to inhibit myelination if present in excess. These studies identify FGF9-dependent signal transduction in astrocytes as a novel target for therapeutic strategies designed to enhance remyelination by endogenous OPC in MS.

overall_design: Gene expression profiles of rat myelinating cultures grown in the presence or absence of FGF9 (100 ng/ml) for 24h and 10 days were generated using Affymetrix GeneChip® Rat Gene 1.0 ST Arrays. Each time point (T1: 24 hrs, and T2: 10 days) has Control (CTR) and Treatment (FGF) groups, with two replicates in each group. In total, 8 arrays were generated from the four groups (CTR-T1, CTR-T2, FGF-T1 and FGF-T2).

first: Christopher

last: Linington


title: Identification of the long, edited dsRNAome in LPS-stimulated primary human peripheral blood monocytes

status: Public on Apr 14 2016

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

type: Expression profiling by high throughput sequencing

summary: Endogenous double-stranded RNA (dsRNA) is intricately regulated in mammals to prevent aberrant activation of host inflammatory pathways by cytosolic dsRNA binding proteins. We define the endogenous dsRNA repertoire in human peripheral blood monocytes using published data (GSE60216) derived from 18 RNA-Seq experiments from neonates, adults, and elderly patients during the inflammatory response to bacterial lipopolysaccharide. Editing by adenosine deaminases that act of RNA (ADAR) enzymes was quantified temporally using this RNA-Seq data to identify 3,438 Editing Enriched Regions (EERs), indicative of highly structured dsRNA. Nearly all human EERs were present in introns. A comparison of EERs from mouse and human revealed significant conservation of EERs between mouse EER- associated genes and homologous human genes.

overall_design:
This Series represents a re-analysis of Samples (GSM1467783-GSM1467809) submitted by another user.
All reads were aligned to the human genome (hg19) using GNUMAP-bs. GNUMAP-bs was run with arguments “--lib_type wt1 --read_type rna --num_threads 12 --mpi 0 -- 17  nt_conv a2i --top_k_hash 10 --map_quality sensitive.” All alignments for a given biological sample (neonate 0 hr, neonate 1 hr, neonate 6 hr, adult 0 hr, etc...) were merged into one alignment file and filtered using the Useq application SamTranscriptomParser. For GNUMAP alignments, the following command options were used: -a 10000 -n 1000000 -p -r. Alignments were converted to pileup format using samtools (Version 0.1.19) mpileup with the command options "-A -B -Q 13". Pileup files were parsed using the Useq (Version 8.7.9) application RNAEditingPileupParser with the comman options "-v H_sapiens_Feb_2009 -t -m". The USeq application RNAEditingScanSeqs with command options "-t -i" was used to detect editing enriched windows from RNAEditingPileupParser point data. The USeq application EnrichedRegionMaker with command options "-I 0 -s 3-g 2500" generated initial lists of EERs. All regions with less than 2 editing-enriched windows were discarded.

first: Brenda

last: Bass


title: miR-132 mediates renal fibrosis: Genome-wide analysis of gene expression in foxd1-derivative interstital cells derived from fibrotic kidneys from mice treated with antagomir-132 or scramblemir

status: Public on Feb 16 2016

city: Leiden

first: Roel

last: Bijkerk

address: Albinusdreef 2

department: Nephrology

institute: LUMC

summary: Chronic kidney disease is associated with progressive renal fibrosis, where perivascular cells give rise to the majority of α-SMA positive myofibroblasts. We sought to identify pericytic miRNAs that could serve as a target to decrease myofibroblast formation. We induced kidney fibrosis in FoxD1-GC;Z/Red-mice by unilateral ureteral obstruction (UUO) followed by FACS sorting of dsRed-positive FoxD1-derivative cells and miRNA profiling. MiR-132 selectively increased 21-fold during pericyte-to-myofibroblast formation whereas miR-132 was only 2.5-fold up in total kidney lysates (both in UUO and ischemia-reperfusion injury). MiR-132 silencing in UUO decreased collagen deposition (35%) and tubular apoptosis. Immunohistochemistry, western blot and qRT-PCR confirmed a similar decrease in interstitial α-SMA+ cells. Pathway analysis identified a rate-limiting role for miR-132 in myofibroblast proliferation that was confirmed in vitro. Indeed, antagomir-132 treated mice displayed a reduction in the number of proliferating, ki67+ interstitial myofibroblasts. Interestingly, this was selective for the interstitial compartment and did not impair the reparative proliferation of tubular epithelial cells, as evidenced by an increase in ki67+ epithelial cells, as well as increased (p-)RB1, Cyclin-A and decreased RASA1, p21 levels in kidney lysates. Taken together, silencing miR-132 counteracts the progression of renal fibrosis by selectively decreasing myofibroblast proliferation and could potentially serve as a novel antifibrotic therapy.

overall_design: Total RNA obtained from FACS sorted mouse renal FoxD1-derivatve interstitial cells from mice that were treated with antagomir-132 or scramblemir and underwent UUO (n=4)

first: Anton

last: van Zonneveld


title: Classifying the Canine B-cell Lymphoma Cell line CLBL1

status: Public on May 05 2016

city: Columbus

first: Bonnie

middle: Kate

last: Harrington

institute: Ohio State University

type:
Expression profiling by array
Third-party reanalysis

summary: In 2013, Richards, et al. reported in Cancer Research that canine b-cell lymphomas could be subclassificed by gene expression profiling as ABC-like or GCB-like, similar to their human diffuse large B-cell lymphomas. This study, therefore, sought to classify the cell line CLBL1 as either GCB or ABC.

overall_design: We downloaded supplementary microarray data (GSE43664) from GEO and then merged the microarray data for CLBL1 and processed the combined data using the robust multiarray averaging (RMA) method in version 3.1.2 of the R statistical programming environment.

first: William

last: Kisseberth


title: Impact of Verteporfin on HCC cells

status: Public on Feb 11 2016

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Together with TEAD4 the Hippo pathway effector YAP stimulates chromosomal instability. Verteporfin is known to disrupt the physical YAP/TEAD interaction and tehrefore might prevent from chromosomal instability in liver cancer.

overall_design: Immortalized HCC cell line hepG2 is treated with Verteporfin for 24 hours.

first: Kai

last: Breuhahn


title: DNA methylation and hormone receptor status in breast cancer, the BCCC study

status: Public on Feb 12 2016

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary:
Genome wide DNA methylation profiling of invasive breast cancer samples isolated from an ethnically diverse group of 80 patients in the Breast Cancer Care in Chicago (BCCC) study. DNA was extracted from formalin fixed, paraffin-embedded samples on 80 patients (21 White, 31 African-American, 23 Hispanic and 5 not reported) (training dataset) enrolled in the BCCC. Hormone receptor status was defined as negative if tumors were negative for both estrogen and progesterone (ER/PR) receptors (N=22/75).
Formalin-fixed, paraffin-embedded (FFPE) tumor samples came from the Breast Cancer Care in Chicago (BCCC) study (Dookeran KA, Silva A, Warnecke RB, Rauscher GH: Race/ethnicity and disparities in mastectomy practice in the Breast Cancer Care in Chicago study. Ann Surg Oncol 2015, 22:66–74). Copies of pathology reports and the corresponding set of Hematoxylin and Eosin (H&E) stained slides were requested from the pathology department at each diagnosing institution, and a single pathologist selected tumor blocks representative of the tumor. Two recuts (at 4 µm each) were made from each selected block for H&E staining. The recuts were then examined in order to identify invasive components of the sample, and areas were marked according to tissue component. Cores of invasive tissue (2 mm in diameter) were obtained from the marked areas and DNA was extracted for the DNA methylation study.

overall_design: Bisulphite converted DNA from the 80 samples were hybridised to the Illumina GoldenGate Methylation Cancer Panel I

first: Garth

last: Rauscher


title: Blood Gene Expression Profiling of an Early Acetaminophen Response (II)

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

summary: Acetaminophen can adversely affect the liver especially when overdosed.  We used whole blood as a surrogate to identify genes as potential early indicators of an acetaminophen-induced response.  In a clinical study, healthy human subjects were dosed daily with 4g of either acetaminophen or placebo pills for 7 days and evaluated over the course of 14 days.  Alanine aminotransferase (ALT) levels for responders to acetaminophen increased between days 4 and 9 after dosing and 12 genes were detected with expression profiles significantly altered within 24hrs. The early responsive genes separated the subjects by class and dose period.  In addition, the genes clustered patients who overdosed on acetaminophen apart from controls and also predicted the exposure classifications with 100% accuracy.  The responsive genes serve as early indicators of an acetaminophen exposure and their gene expression profiles can potentially be evaluated as molecular indicators for further consideration.

overall_design: Overdosed patients admitted to the emergency room.  Five male and female individuals from 19 - 59 years old were admitted to the emergency room following an overdose on acetaminophen. The patients presented 12hrs to 4 days after ingestion. ALT and AST  elevated peaking beyond 400 U/I and 120 U/I.  Blood was collected 2 or 5 days following ingestion.

middle: R

first: Richard

middle: S

last: Paules


title: Blood Gene Expression Profiling of an Early Acetaminophen Response (I)

overall_design: Randomized, single-blind, placebo-controlled, clinical study.  Healthy male and female individuals from 18 – 58 years old weighing 55 kg to 85 kg volunteered as subjects in the study. Subjects were enrolled for 14 days each and were acclimated for 3 days on a controlled, standardized whole-food diet in order to assure a uniform nutritional intake. Starting on day 0 and until day 7 relative to the start of dosing, each subject received daily repeat dosing every 6 hrs (i.e. 4x daily) of either 1g of acetaminophen or placebo pills orally.  Blood was collected at 8 a.m. on each day of the clinical study for alanine aminotransferase (ALT) measurement and complete blood counts (CBC).


title: Blood Gene Expression Profiling of an Early Acetaminophen Response

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

overall_design: Refer to individual Series


title: Daptomycin tolerance in the Staphylococcus aureus pitA6 mutant is due to upregulation of the dlt-operon

status: Public on Feb 10 2016

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary: It is very important to understand the mechanisms how bacteria become tolerant towards antibiotics during clinical therapy. In a previous study we showed that increased daptomycin (DAP) tolerance of Staphylococcus aureus was due to a point mutation in pitA (inorganic phosphate transporter) that led to intracellular accumulation of both inorganic phosphate (Pi) and polyphosphate (polyP). DAP tolerance in that pitA6 mutant differs from classical resistance mechanisms as there was no increase in minimal inhibitory concentration (MIC). In this study we demonstrate that DAP tolerance in the pitA6 mutant is not triggered by the accumulation of polyP. Transcriptome analysis revealed that about 234 genes were at least 2.0-fold differently expressed in the mutant. Particularly, genes involved in protein biosynthesis, carbohydrate and lipid metabolism as well as in replication and maintenance of DNA were downregulated. However, the most important change was the upregulation of the dlt-operon, which is induced by the accumulation of intracellular Pi. The GraXRS system, known as activator of both dlt and mprF, as well as surface charge, cell wall thickness or the content of wall teichoic acids (WTA) are not involved in DAP tolerance in the pitA6 mutant. In conclusion the DAP tolerance in the pitA6 mutant is due to an upregulation of the dlt-operon triggered directly or indirectly by the accumulation of Pi.

overall_design: WT strain HG003 and its pitA mutant were used to compare transcriptomic changes after 6 or 8 hours of growth in suspension in TSB medium

first: Lukas

last: Mechler

first: Eve-julie

last: Bonetti

first: Sebastian

last: Reichert

first: Matthias

last: Flötenmeyer

first: Jacques

last: Schrenzel

first: Ralph

last: Bertram

first: Patrice

last: François

first: Friederich

last: Goetz


title: miRNA gene expression in the pseudoglandular phase

status: Public on Feb 05 2016

city: Boston

first: Mauro

last: Longoni

state: MA

address: 185 Cambridge Street

department: Pediatric Surgical Research Laboratories

institute: Massachusetts General Hospital

summary: MicroRNA expression levels were assessed during the pseudoglandular phase of normal fetal lung development at the critical time, when the the conducting airways are formed. Precise miRNA regulation is important for proper pulmonary organogenesis, supporting the delicate balance between expansion of progenitor cells and their terminal differentiation. Microarray analyses could indicate the potential involvement of miRNAs important for human pulmonary hypoplasia.

overall_design: Two replicates of pooled RNA from two 9 week old fetal lung samples

first: Ethan

last: Sanford

first: Kwongwai

last: Choy

first: Maria

last: Loscertales


title: Genome-wide analysis of Prz1 in fission yeast reveals a novel inhibitory role in flocculation and a conserved activating role in cell wall organization [ChIP-chip]

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive NW

department: Biological Sciences

institute: University of Calgary

type: Genome binding/occupancy profiling by genome tiling array

summary: Gene regulation in response to intracellular calcium is mediated by the calcineurin-activated transcription factor Prz1 in the fission yeast Schizosaccharomyces pombe. Genome-wide studies of the Crz1 and CrzA fungal orthologs have uncovered numerous target genes involved in conserved and species-specific cellular processes. In contrast, very few target genes of Prz1 have been published. This paper identified an extensive list of genes using transcriptome and ChIP-chip analyses under inducing conditions of Prz1, including CaCl2, and tunicamycin treatment, as well as a ∆pmr1 genetic background. We identified 165 upregulated putative target genes of Prz1 in which the majority contained a calcium-dependent response element in their promoters, similar to that of the Saccharomyces cerevisiae ortholog Crz1. These genes were functionally enriched for Crz1-conserved processes such as cell wall biosynthesis. Overexpression of prz1+ increased resistance to the cell wall degradation enzyme zymolyase, likely from upregulation of the O-mannosyltransferase encoding gene omh1+. Loss of omh1+ abrogates this phenotype. We uncovered a novel inhibitory role in flocculation for Prz1. Loss of prz1+ resulted in constitutive flocculation and upregulation of genes encoding the flocculins Gsf2 and Pfl3, as well as the transcription factor Cbf12. The constitutive flocculation of the ∆prz1 strain was abrogated by the loss of gsf2+ or cbf12+. This study reveals that Prz1 functions as a positive and negative transcriptional regulator of genes involved in cell wall biosynthesis and flocculation, respectively. Moreover, comparison of target genes between Crz1/CrzA and Prz1 indicate some conservation in DNA-binding specificity, but also substantial rewiring of the calcineurin-mediated transcriptional-regulatory network.

overall_design: We generated 2 ChIP-chip experiments, each with a biological replicate performed as a dye swap.

first: Kate

last: Chatfield-Reed

first: Lianne

last: Vachon

first: Eun-Joo

last: Kwon


title: Genome-wide analysis of Prz1 in fission yeast reveals a novel inhibitory role in flocculation and a conserved activating role in cell wall organization [expression]

overall_design: We generated 3 overexpression microarrays and 2 deletion microarrays with dye swaps, and 2 deletion microarrays with drug treatments with dye swaps, each with a biological replicate performed as a dye swap. The effect of the mutant strains were all compared to wild type or empty vector strains, except for one experiment where the prz1 deletion mutant was compared to the pmr1 deletion mutant.


title: miRNA expression in the canalicular phase of  human lung development

summary: MicroRNA expression levels were assessed during the canalicular phase of normal fetal lung development at the critical time, when the distal airway epithelium proliferates and differentiates. Precise miRNA regulation is important for proper pulmonary organogenesis, supporting the delicate balance between expansion of progenitor cells and their terminal differentiation. Microarray analyses could indicate the potential involvement of miRNAs important for human pulmonary hypoplasia.

overall_design: Two replicates of pooled RNA from two 18-20 week old fetal lung samples


title: Conserved and diverged functions of the calcineurin-activated Prz1 transcription factor in fission yeast


title: Aberrant epigenetic regulation in clear cell sarcoma of the kidney (CCSK)

status: Public on Feb 04 2016

city: Lund

first: Jenny

last: Karlsson

address: BMC C13

department: Clinical genetics

country: Sweden

institute: Lund University

summary:
Methylation array analyses of 30 CCSKs in comparison with 18 Wilms tumours and normal non-malignant kidneys (2 foetal kidneys and 6 adult kidneys) revealed CCSK tumour DNA to be globally hypermethylated.
Four CCSKs, two WTs, two foetal kidneys and 2 adult kidneys were analysed as technical duplicates on different arrays.

overall_design: Bisulphite converted DNA was hybridised to the Illumina Infinium HumanMethylation27k array at the SCIBLU Lund University Sweden (http://www.lth.se/sciblu). The samples were analysed on three different arrays.

first: Anders

last: Valind

first: Caroline

last: Jansson

first: Maureen

middle: J

last: O’Sullivan

first: Linda

last: Holmquist Mengelbier

first: David

last: Gisselsson


title: microRNA expression levels during the pseudoglandular to canalicular phase transition of fetal lung development


title: Combined Genetic and Genealogic Studies Uncover a Large BAP1 Cancer Syndrome Kindred Tracing Back Nine Generations to a Common Ancestor from the 1700s.

status: Public on Feb 03 2016

city: Honolulu

first: Michele

last: Carbone

state: HI

address: 701 Ilalo Street, Room 437

institute: University of Hawaii Cancer Center

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

summary: We recently discovered an inherited cancer syndrome caused by BRCA1-Associated Protein 1 (BAP1) germline mutations with high incidence of mesothelioma, uveal melanoma and other cancers and very high penetrance by age 55. To identify families with the BAP1 cancer syndrome, we screened patients with family histories of multiple mesotheliomas and melanomas and/or multiple cancers. We identified four families that shared an identical BAP1 mutation: they lived across the US and did not appear to be related. By combining family histories, molecular genetics, and genealogical approaches, we uncovered a BAP1 cancer syndrome kindred of ~80,000 descendants with a core of 91 individuals, whose members descend from a couple born in Germany in the early 1700s who immigrated to North America. Their descendants spread throughout the country with mutation carriers affected by multiple malignancies.  Our data show that, once a proband is identified, extended analyses of these kindreds, using genomic and genealogical studies to identify the most recent common ancestor, allow investigators to uncover additional branches of the family that may carry BAP1 mutations. Using this knowledge, we have identified new branches of this family carrying BAP1 mutations. We have also implemented early-detection strategies that help identify cancers at early-stage, when they can be cured (melanomas) or are more susceptible to therapy (MM and other malignancies).

overall_design: Mesothelioma patients with family histories including multiple mesotheliomas and melanomas and/or multiple cancers were screened for mutations in BAP1.  Four apparently un-related individuals were identified that carried an identical truncating mutation in BAP1 that was not present in any examined genetic database.  To identify whether the mutation was inherited-by-descent from a common ancestor, the four subjects and four normal donors were genotyped using genome-wide Ilumina micro-arrays from which principal component, identity-by-descent, and shared haplotype analyses were performed.

first: Erin

last: Flores

first: Mitsuru

last: Emi

first: Todd

last: Johnson

first: Tatsuhiko

last: Tsunoda

first: Dusty

last: Behner

first: Harriet

last: Hoffman

first: Masaki

last: Nasu

first: Andrea

last: Napolitano

first: Amy

last: Powers

first: Michael

last: Minaai

first: Francine

last: Baumann

first: Peter

last: Bryant-Greenwood

first: Olivia

last: Lauk

first: Michaela

last: Kirschner

first: Walter

last: Weder

first: Isabelle

last: Opitz

first: Harvey

middle: I

last: Pass

first: Giovanni

last: Gaudino

first: Sandra

last: Pastorino

first: Haining

last: Yang


title: Genomic instability in human embryonic stem cells is associated to culture density and medium acidification.

status: Public on Feb 02 2016

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

summary: Human embryonic stem cells (hESC) show great promise for clinical and research applications, but genomic instability hampers the development of their full potential. Here we demonstrate that increased culture density causes medium acidification due to lactic acid accumulation. hESC are able to cope with this, but acquire increased DNA damage associated to DNA replication stress. Also, single-cell genomics analysis reveals a strong correlation of the occurrence of de novo CNVs and culture density after only five days of culture. However, by an improved control over the accumulation of metabolites through more frequent medium changes, we were able to counter the effect of culture density on DNA damage and CNVs. These data underline the importance of optimal culture conditions, even at short-term, in the light of bringing hESC to their full potential.

overall_design: We isolated 29 single hESC from the lowest density group (A) and 30 of the highest-density group (D) and compared CNV occurence at a resolution of 7 consecutive clones.

first: K

first: M

last: Geens

first: A

last: Mertzanidou

first: I

last: Smolders

first: H

last: Nguyen

first: J

last: Smitz

first: C

last: Spits


title: Genome-wide association study on craniofacial microsomia

city: Beijing

first: Yong-Biao

last: Zhang

state: Select a State or Province

address: Beichen west road 1#

institute: Beijing Institute of Genomics

summary: Craniofacial microsomia encapsulates congenital anomalies of the external and middle ear, maxilla, mandible, facial and trigeminal nerves, and surrounding soft tissues on the affected side. The recruitment of craniofacial microsomia samples is a huge problem to bind the investigation of its genetic basis because of the lower prevalence rate (ranging between 1 and 4 per 10,000 births) and consultation rate. Here, we performed the first genome-wide associations study on craniofacial microsomia and identified many significant loci associated with craniofacial microsomia.

overall_design: To investigate the loci associated with craniofacial microsomia, we performed GWAS on patients from China .

first: Qing-Guo


title: miR-126 Governs Human Leukemia Stem Cell Quiescence and Therapeutic Resistance [miRNA]

city: Toronto

first: John

middle: E

last: Dick

address: 101 College St. Toronto

institute: Ontario Cancer Institute

summary: In acute myeloid leukemia (AML), leukemia stem cells (LSC) play a central role in disease progression and recurrence due to their intrinsic capacity for self-renewal and chemotherapy resistance. Whereas epigenetic mechanisms balance normal blood stem cell self-renewal and fate decisions, mutation and dysregulation of epigenetic regulators are considered fundamental to leukemia initiation and progression. Alterations in miRNA function represent a non-canonical epigenetic mechanism influencing malignant hematopoiesis, however the function of miRNA in human LSC remains undetermined. Here we show that miRNA profiling of fractionated AML populations defines an LSC-specific signature that is highly prognostic for patient survival. Gain- and loss-of-function analyses demonstrated that miR-126 restrained cell cycle progression, prevented differentiation, and increased self-renewal of human LSC. By targeting the G0 to G1 gatekeeper CDK3, miR-126 preserved LSC quiescence and promoted chemotherapy resistance. Thus, in AML, miRNAs influence patient outcome through post-transcriptional regulation of stemness programs in LSC.

overall_design: Peripheral blood from 24 AML patients and 3 human lin-CB pools were thawed, stained for CD34/CD38 cell surface markers and sorted into 4 populations.  A total of 13 AML patient samples were functionally validated for leukemia-initiating capacity by xenotransplanation into immunodeficient mice.  Global miRNA profiling was performed on all sorted AML samples and 3 lin-CB samples.  An LSC miRNA signature was derived by infomatically testing engrafting fractions against non-engrafting fractions.

first: Eric

last: Lechman

first: Jun

last: Lu

first: Veronique

last: Voisan


title: TRANSCRIPTOMIC ANALYSIS OF BOTTLENOSE DOLPHIN (Tursiops truncatus) SKIN BIOPSIES TO ASSESS THE EFFECTS OF EMERGING CONTAMINANTS ON A TOP PREDATOR IN THE MEDITERRANEAN SEA

status: Public on Feb 01 2016

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

institute: University of Ferrara

summary: To assess the impact of emerging contaminats on dolphin transcriptome

overall_design: Collection of skin biopsy from wild dolphin in Tuscany (Italy) and analysis of the differentially expressed genes upon treatmens with emerging contaminants (BPA and PFOA)


title: miRNA analysis in myofibroblasts derived from normal oesophagus and esophageal cancers

city: Liverpool

first: Liyi

last: Wang

state: Merseyside

address: Crown Street

department: Department of Physiology

institute: University of Liverpool

summary: We prepared miRNA from myofibroblats derived from normal oesophagus  and esophageal cancers. miRCURYTM LNA Array ver5 was performed and comparisons were made by the dual (reference) method.

overall_design:
Briefly, we have myofibroblast (NTM) from normal stomach and oesophagus, and we would like to establish whether there is tissue specific myofibroblast miRNA signature.
Within the stomach (gastric) we made myofibroblasts from cancer (CAM) and adjacent tissue (ATM) from the same patients and myofibroblasts from healthy individuals (NTM) and we want to compare the matching ones paired and the total numbers unpaired.
We have the same experimental design within the oesophagus but there we have two types of cancers (squamous and adenocarcinoma) so we wanted to do them separately for the two different groups and all together.
In order to facilitate comparisons within each tissue type, we have used a different common reference for each tissue, and to compare between tissues using single colour analysis.
Dual reference method was used to compare samples within a tissue and singe channel (quantile method) was used to compare samples across tissues.


title: miRNA profiling of oesophageal and gastric myofibroblast in health and disease


title: Truncating erythropoietin receptor rearrangements in acute lymphoblastic leukemia

city: Memphis

first: Charles

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

summary:
Chromosomal rearrangements are a hallmark of acute lymphoblastic leukemia (ALL) and are important ALL initiating events. We describe four different rearrangements of the erythropoietin receptor gene EPOR in Philadelphia
chromosome-like (Ph-like) ALL. All of these rearrangements result in truncation of the cytoplasmic tail of EPOR at residues similar to those mutated in primary familial congenital polycythemia, with preservation of the proximal tyrosine essential for receptor activation and loss of distal regulatory residues. This
resulted in deregulated EPOR expression, hypersensitivity to erythropoietin stimulation, and heightened JAK-STAT activation. Expression of truncated EPOR in mouse B cell progenitors induced ALL in vivo. Human leukemic cells with EPOR rearrangements were sensitive to JAK-STAT inhibition, suggesting a therapeutic
option in high-risk ALL.

overall_design: Mice expressing truncated EPOR were analyzed

first: Ilaria

last: Iacobucci

first: Yongjin

last: Li


title: Identification of CdnL, a putative transcriptional regulator involved in repair and outgrowth of heat-damaged Bacillus cereus spores

city: Ede

first: Jos

last: Boekhorst

address: Kernhemseweg 2

institute: NIZO food research

summary:
Heat-treated spores show delayed and slower germination and outgrowth compared to untreated spores presumably due to spore damage repair. This study was performed to identify genes possibly involved in spore damage repair in B. cereus.
In this study we compared the transcriptomic profiles of untreated and heat-treated spores during germination and outgrowth in BHI at 30C.

overall_design: Matrix is compatible with the Agilent-017343 array design. Elermeiers with BHI were inoculated with untreated or heat-treated (1 min at 95C) B. cereus spores (final volume 20ml, final spore concentration 10^8 sp/ml) and incubated with aeration (200rpm) at 30C untill harvesting. Elermeiers were harvested for untreated spores 10, 20, 30 and 50 min and for heat-treated 50, 90, 120 and 150 minutes after adding BHI. Samples from experimental duplicates were hybridized on the arrays with at least 3 technical replicates for each experimantal replicate.

first: Alicja

middle: K

last: Warda

first: Marcel

last: Tempelaars

first: Tjakko

last: Abee

first: Masja

middle: N

last: Nierop Groot


title: miRNA analysis in myofibroblats derived from normal stomach, both antrum (A) and corpus (C) separately and gastric cancers

summary: We prepared miRNA from myofibroblats derived from normal stomach, both antrum (A) and corpus (C) separately and gastric cancers. miRCURYTM LNA Array ver5 was performed and comparisons were made by the dual (reference) method.


title: Gene and microRNA expression profiling of a melanoma cell line resistant to BRAF inhibitor PLX4032 compared to the parental sensitive counterpart (miRNA)

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: Gene and microRNA expression profiles were generated for a melanoma cell line resistant to the BRAF inhibitor PLX4032 and its parental cell line in order to identify altered gene-microRNA regulatory networks. Results showed that CCL2 acts as an autocrine factor and coordinately regulates, via HIF1, miR-34a, miR-100 and miR-125b, which are involved in cell proliferation and apoptosis. Inhibition of CCL2 and of the specific miRNAs restores sensitivity to BRAF inhibitors.

overall_design: Four biological replicates for resistant and parental cells were generated by independent cultures and RNA extractions. Profiles of resistant and parental cell lines were compared to identify differentially expressed microRNAs.

first: Elisabetta

last: Vergani

first: Monica

last: Rodolfo


title: Gene and microRNA expression profiling of a melanoma cell line resistant to BRAF inhibitor PLX4032 compared to the parental sensitive counterpart (mRNA)

overall_design: Four biological replicates for resistant and parental cells were generated by independent cultures and RNA extractions. After quality control one sample from the gene expression dataset was discarded for poor gene expression profile quality.


title: Real-time quantitative PCR analysis of microRNA expression in neonatal cardiovascular progenitors before and after 7 Days of simulated microgravity.

city: Loma Linda

first: Mary

last: Kearns-Jonker

state: CA

address: 25094 Daisy Ave

department: Anatomy

institute: Loma Linda University

summary: Human cardiovascular progenitors were isolated from neonatal (<1 month old) atrial tissue and cloned by single cell dilution.  MicroRNA expression in neonatal cardiovascular progenitor cell (CPC) clones was compared before and after exposure to simulated microgravity using sabiosciences cell development & differentiation miRNA PCR array.

overall_design: MicroRNA expression profiling by RT-PCR,  3 neonatal cardiac progenitor cell clones were run separately and fold changes were then pooled and compared before and after simulated microgravity exposure.

first: Tania

last: Fuentes


title: Gene and microRNA expression profiling of a melanoma cell line resistant to BRAF inhibitor PLX4032 compared to the parental sensitive counterpart

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

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

overall_design: Refer to individual Series


title: LncRNAs expression signatures of cumulus cells isolated from PCOS patients revealed by microarray

city: Shanghai

first: Xin

last: Huang

state: Shanghai

address: No.2699 Gaoke east road

department: Reproductive Medicine Centre

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

summary: Our study is the first one to determine genome-wide lncRNAs expression patterns in cumulus cells of PCOS patients by microarray. The results displayed that clusters of lncRNAs (n=623) were aberrantly expressed in PCOS patients compared with non-PCOS patients. Many differentially expressed lncRNAs were transcribed from regions on chromosome 2 and classified into enhancer-like lncRNA subgroup. XLOC_011402 (PWRN2) was found for the first time that it was not only expressed in testis but also in cumulus cells. All the results revealed that lncRNAs differentially expressed in cumulus cells may exert a partial or key role in hormone abnormalities of PCOS patients and maybe impact on oocyte development. Taken together, this study may provide potential targets for further treatment of PCOS and novel insights into oocyte development.

overall_design: we described lncRNAs profiles in cumulus cells isolated from ten patients (5 PCOS and 5 non-PCOS patients) by microarray. with abundant and varied probes accounting about 39,000 human lncRNAs in our microarray, the number of lncRNAs that expressed at a certain level could be detected is 24292. From the data, we found 623 lncRNAs were significantly up-regulated or down-reguated, which could be used to discriminate PCOS from non-PCOS cumulus cells (≥2-fold). Of them, the up-regulated lncRNAs (n=620) were more common than down-regualted ones (n=3). In addition, the distribution of the differentially expressed lncRNAs was unbalance in all human chromosomes, i.e. there are 74 lncRNAs were transcribed from regions on chromosome 2 while only 7 lncRNAs were transcripts from regions on chromosome 22. Further analysis showed the differentially expressed lncRNAs were classified into three subgroups: HOX loci lncRNAs (n=2), Enhancer-like lncRNAs (n=87) and lincRNAs (n=6). Five differentially expressed lncRNAs (XLOC_011402, ENST00000454271, ENST00000433673, ENST00000450294, and ENST00000432431) were selected to validate of the microarray results by quantitative RT-PCR in both the original samples for the microarray analysis and a cohort of cumulus cells samples isolated from the additional 30 PCOS and 30 non-PCOS patients. All the qRT-PCR results were consistent with the microarray data.


title: miR-126 governs human leukemia stem cell quiescence and therapeutic resistance

first: Stanley

last: Ng

state: Ontario

address: 160 College Street

institute: Univerity of Toronto

summary: In acute myeloid leukemia (AML), leukemia stem cells (LSC) play a central role in disease progression and recurrence due to their intrinsic capacity for self-renewal and chemotherapy resistance. Whereas epigenetic regulation balances normal blood stem cell self-renewal and fate decisions, mutation and dysregulation of epigenetic modifiers are now considered fundamental to leukemia initiation and progression. Alterations in miRNA function represent a non-canonical epigenetic mechanism influencing malignant hematopoiesis, however the function of miRNA in LSC remains undetermined. Here we show that miRNA profiling of fractionated AML populations defines an LSC-specific signature that is highly predictive of patient survival. Gain of function genetic analysis demonstrated that miR-126 restrained cell cycle progression, prevented LSC differentiation, and increased LSC self-renewal. miR-126 promoted chemo-resistance,  preserving LSC quiescence in part through suppression of the G0 to G1 gatekeeper, CDK3. Thus, in AML, miRNAs influence patient outcome through post-transcriptional regulation of stemness programs in LSC.

overall_design: 74 primary patient normal karyotype AML samples were analyzed for miRNA expression.

first: Eric

last: Lechman

first: Berhard

last: Gentner

first: Peter

last: van Galen

first: Silvia

last: Nucera

middle: W

first: James

last: Kennedy

first: Amanda

last: Mitchell

first: Weihsu

middle: C

last: Chen

first: Bjorn

last: Nilsson

first: Kolja

last: Eppert

first: Rene

last: Marke

first: Liran

last: Shlush

first: Veronique

last: Voisin

first: Gary

middle: D

last: Bader

last: Zandstra

first: Milan

last: Clinician

first: Todd

last: Golub

first: Benjamin

middle: L

last: Ebert

first: Jun

last: Lu

first: Mark

last: Minden

first: Jean

middle: Y

first: Luigi

last: Naldini

first: John

last: Dick