title: Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells [DamID]

status: Public on Mar 10 2015

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary: In mammals, the nuclear lamina interacts with hundreds of large genomic regions, termed lamina-associated domains (LADs) that are generally in a transcriptionally repressed state. Lamins form the major structural component of the lamina and have been reported to bind DNA and chromatin. Here we systematically evaluated whether lamins are necessary for the peripheral localization of LADs in murine embryonic stem cells. Surprisingly, removal of essentially all lamins did not have any detectable effect on the genome-wide interaction pattern of chromatin with the inner nuclear membrane. This suggests that other components of the inner nuclear membrane mediate these interactions.

overall_design: DamID for Emerin and lamin A were performed in different mouse ESC background: wild type (wt), B lamins null (dKO), B lamins null and A lamins knockdown (tKO). For each cell-type there were 2 biological replicates, that were hybridized in a dye-swap design.

first: Mario

last: Amendola


title: MiRNA Expression Analysis of Intraductal Papillary Mucinous Neoplasms (IPMNs) of the Pancreas

status: Public on Jan 29 2015

city: Tampa

first: Jennifer

middle: Permuth

last: Wey

state: FL

address: 12902 Magnolia Dr

country: USA

institute: Moffitt Cancer Center

summary: To discover a panel of mi(cro)RNAs that accurately differentiate between high-risk IPMN tissue (from pathologically-confirmed invasive or high-grade IPMN cases) and low-risk IPMN tissue (from pathologically-confirmed low-or moderate-grade IPMN cases).

overall_design: In a discovery phase, genome-wide miRNA expression profiling was performed on 28 surgically-resected, pathologically-confirmed IPMNs (19 high-risk, 9 low-risk) using Taqman Low Density Arrays.  A validation phase was performed in 21 independent IPMNs (13 high-risk, 8 low-risk).  We also explored genes regulated by the identified miRNAs by integrating microarray expression data from 23 IPMNs.

middle: P


title: Transcriptome comparison between CHOPS syndrome and Cornelia de Lange syndrome

status: Public on Jan 27 2015

city: Philadelphia

first: IAN

middle: D.

last: KRANTZ

state: PA

address: 34th and Civic Blvd.

department: Division of Human and Molecular Genetics

institute: The Children's Hospital of Philadelphia

summary: CHOPS syndrome is caused by germline gain-of-function mutations of AFF4.  Cornelia de Lange syndrome is caused by germline mutations of cohesin loading factors or cohesin complex genes such as NIPBL, SMC1A, SMC3 and HDAC8.  There are many overlapping clinical features exist between CHOPS syndrome and Cornelia de Lange syndrome. To identified commonly dysregulated genes in CHOPS syndrome and Cornelia de Lange syndrome, we perfomred side-by-side transcriptome comparison between CHOPS syndrome and Cornelia de Lange syndrome.

overall_design: In this transcriptome analysis, patient derived skin fibroblasts from two CHOPS syndrome probands, two Cornelia de Lange syndrome probands, and four age-gender-ethnicity matched healthy control subjects were used.The samples used for Human Gene 2.0 arrays are two CHOPs syndrome samples (CDL160 and CDL444), two Cornelia de Lange syndrome samples (CdL006: 7 year-old Caucasian female  NIPBL 742_743delCT ;L248TfsX6 and CdL015: 10 year-old Caucasian male NIPBL 2969delG;G990DfsX2), and four age gender matched control samples (GM01652, GM01864, GM02036 and GM03348).

first: Kosuke

last: Izumi

first: Zhe

last: Zhang

first: Andrew

middle: C

last: Edmondson

first: Sarah

last: Noon

first: Matthew

last: Dulik

first: Ramkakrishnan

last: Rajagopalan

middle: A

last: Deardorff

first: Dinah

last: Clark

first: Maninder

last: Kaur

first: Ian

middle: D

last: Krantz


title: Gene expression profile of hemocytes from Drosophila melanogaster on lipid-enriched diet compared to normal diet

status: Public on Jan 30 2015

city: London

first: Katrin

last: Kierdorf

address: New Maze Pond

country: United Kingdom

institute: King's College London

summary: Long-term consumption of fatty foods is associated with obesity, macrophage  activation and inflammation, metabolic imbalance, and a reduced lifespan. We took  advantage of Drosophila genetics to investigate the role of macrophages and the  pathway(s) that govern their response to dietary stress. Flies fed a lipid-rich diet  presented with increased fat storage, systemic JAK-STAT activation, reduced insulin  sensitivity and hyperglycaemia, and a shorter lifespan. Drosophila macrophages  scavenged lipids and produced the type 1 cytokine upd3, in a scavenger-receptor  (croquemort) and JNK-dependent manner. Genetic depletion of macrophages, or  macrophage-specific silencing of upd3 decreased JAK-STAT activation and rescued  insulin sensitivity and the lifespan of Drosophila, but did not decrease fat storage.  NF-κB signalling made no contribution to the phenotype observed. These results  identify an evolutionarily conserved ‘scavenger receptor-JNK-Type 1 cytokine’  cassette in macrophages, which controls glucose metabolism and reduces lifespan in  Drosophila maintained on a lipid-rich diet via activation of the JAK-STAT pathway  Long-term consumption of fatty foods is associated with obesity, macrophage  activation and inflammation, metabolic imbalance, and a reduced lifespan. We took  advantage of Drosophila genetics to investigate the role of macrophages and the  pathway(s) that govern their response to dietary stress. Flies fed a lipid-rich diet  presented with increased fat storage, systemic JAK-STAT activation, reduced insulin  sensitivity and hyperglycaemia, and a shorter lifespan. Drosophila macrophages  scavenged lipids and produced the type 1 cytokine upd3, in a scavenger-receptor  (croquemort) and JNK-dependent manner. Genetic depletion of macrophages, or  macrophage-specific silencing of upd3 decreased JAK-STAT activation and rescued  insulin sensitivity and the lifespan of Drosophila, but did not decrease fat storage.  NF-κB signalling made no contribution to the phenotype observed. These results  identify an evolutionarily conserved ‘scavenger receptor-JNK-Type 1 cytokine’  cassette in macrophages, which controls glucose metabolism and reduces lifespan in  Drosophila maintained on a lipid-rich diet via activation of the JAK-STAT pathway

overall_design: 5 biological samples were FACS-sorted from different batches of Drosophila melanogaster males after 30 days on 15% lipid enriched diet (n=5) and control diet (n=5)

first: Frederic

last: Geissmann

first: Marc

middle: S

last: Dionne

first: Katie

middle: J

last: Woodcock


title: Transcriptome characterization of CHOPS syndrome, a novel genetic disorder caused by gain-of-function mutations of AFF4

summary: AFF4 is a component of super elongation complex (SEC), which plays an important role in mobilizing paused RNA polymerase II at gene promoter regions.  Using exome sequenging, we have identified a novel genetic disorder caused by missense mutations in AFF4.  We propose CHOPS syndrome as a name for this new diagnosis.  To evaluate the effect of identified missense mutations of AFF4, utilizing patient derived skin fibroblast cell lines, the gene expression analysis was perfomred.

overall_design: To characterize the transcriptome pattern observed in CHOPS syndrome, the skin fibroblast samples from two CHOPS syndrome probands and three healthy control subjects were used. Samples used for expression array include two CHOPs syndrome samples (CDL160: 6 year-old Caucasian female with 254S mut and CDL444: 12 year-old Caucasian male with 254A mut) and three age gender matched controls (GM01652: 11 year-old Caucasian female, GM02036 11 year-old Caucasian female and GM08398: 8 year-old Caucasian male).


title: Changes in global gene expression of Vibrio parahaemolyticus viable but non-culturable (VBNC) state

status: Public on Jan 28 2015

city: Berlin

first: Stephan

last: Huehn

address: Koenigsweg 69

country: Germany

institute: Freie Universität Berlin

summary: The phenomenon of viable but non-culturable (VBNC) referred as a dormant state of non-sporulating bacteria enhancing the survival in adverse environments. To our knowledge, only few studies have been performed on whole genomic expression of V. parahaemolyticus in VBNC state compared with cells in exponential and early stationary phases. Since many VBNC state studies found DNA, RNA and protein degradation, we hypothesise that gene regulation of VBNC cells is highly reduced, down-regulation of gene expression is dominant and only metabolic functions crucial for survival are kept on a sustained basis. In the VBNC state we found 509 significantly induced genes and 309 significantly repressed by more than twofold compared with unstressed phases among 4820 investigated genes (adjusted P-value < 0.05). Furthermore, up-regulation was dominant in most of the non-metabolism functional categories, while five metabolism-related functional categories revealed down-regulation in the VBNC state. To our knowledge, this is the first study of comprehensive transcriptomic analyses of three phases of V. parahaemolyticus RIMD2210633. Although the mechanism of VBNC state is not yet clear, massive regulation of gene expression occurs in the VBNC state compared with expression in unstressed phases and thus, VBNC cells are active cells.

overall_design: VBNC state gene expression was detected in total bacterial RNA of V. parahaemolyticus. Three phases (exponential phase, early stationary phase, and VBNC state) were used in 8 biological replicates. Gene expression  in exponential phase and early stationary phase was used for normalization, respectively.

first: Lu

last: Meng

first: Thomas

last: Alter

first: Tommi

last: Aho


title: Global and local gene expression in rice leaves and roots challenged by Magnaporthe oryzae

status: Public on Feb 20 2015

city: Tsukuba

first: Eiichi

last: Minami

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

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

overall_design: Refer to individual Series


title: Expression Profiles of HepG2 cells treated with Cyclosporin A and solvent control

city: Maastricht

first: Wim

last: Van den Hof

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

summary: The transcriptomics changes induced in the human liver cell line HepG2 by Cyclosporin A after treatment for 12h, 24h, 48h and 72h

overall_design: The study investigated differential gene expression in HepG2 cell line mRNA following 12, 24, 48 and 72 hours of exposure to Cyclosporin A and solvent. Three biological replicates per compound/solvent. In total 36 arrays.


title: Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies

first: Daniel

last: Gale

address: Royal Free Hospital, Rowland Hill Street

department: Division of Medicine

institute: University College London

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

summary:
300,000 SNPs genotyped (Illumina CytoSNP12v2 array) in a family with unexplained inherited kidney disease. Analysed using parametric and Combinatorial Conflicting Homozygosity analysis, as described in Levine et al. BMC Genomics 2015.

Abstract: Background: The ability to identify regions of the genome inherited with a dominant trait in one or more families has become increasingly valuable with the wide availability of next generationhigh throughput sequencing technology. While a number of methods exist for mapping of homozygous variants segregating with recessive traits in consanguineous families, dominant conditions are conventionally analysed by by linkage analysis, which requires computationally demanding haplotype reconstruction from marker genotypes and, even using advanced parallel approximation implementations, can take substantial time. In addition, linkage analysis lacks sensitivity in the presence of phenocopies (individuals sharing the trait but not the genetic variant responsible). Combinatorial Conflicting Homozygosity (CCH) analysis uses bi-allelic single nucleotide polymorphism (SNP) marker genotypes to identify genetic loci within which consecutive markers are not homozygous for different alleles. This allows inference of identical by descent (IBD) inheritance of a haplotype among a set or subsets of related or unrelated individuals.  Results: A single genome-wide conflicting homozygosity analysis takes <3 seconds and parallelisation permits multiple combinations of subsets of individuals to be analysed quickly. Analysis of unrelated individuals demonstrated that in the absence of IBD inheritance, runs of no- CH exceeding 4 cM are not observed. At this threshold, CCH is >97% sensitive and specific for IBD regions within a pedigree exceeding this length and was able to identify the locus responsible for a dominantly inherited kidney disease in a Turkish Cypriot family in which 6 six out 17 affected individuals were phenocopies. It also revealed shared ancestry at the disease-linked locus among affected individuals from two different Cypriot populations.   Conclusions: CCH does not require computationally demanding haplotype reconstruction and can detect regions of shared inheritance of a haplotype among subsets of related or unrelated individuals directly from SNP genotype data. In contrast to parametric linkage allowing for phenocopies, CCH directly provides the exact number and identity of individuals sharing each locus. CCH can also identify regions of shared ancestry among ostensibly unrelated individuals who share a trait. CCH is implemented in Python and is freely available (as source code) for download at http://sourceforge.net/projects/cchsnp/.

overall_design: Linkage and identity-by-descent studies in a single family with 17 individuals affected with kidney disease

first: Adam

last: Levine


title: Expression Profiles of microRNAs of HepG2 cells treated with Cyclosporin A and solvent control

summary: The microRNA changes induced in the human liver cell line HepG2 by Cyclosporin A after treatment for 12h, 24h, 48h and 72h

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The study investigated differential microRNA expression in HepG2 cell line following 12, 24, 48 and 72 hours of exposure to Cyclosporin A and solvent. Three biological replicates per compound/solvent. In total 36 arrays .


title: Expression Profiles of mRNAs and microRNAs in HepG2 cells treated with Cyclosporin A and solvent control

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


title: Plasma profiling of miRNAs in mouse model of osteosarcoma.

status: Public on Jan 24 2015

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Osteosarcoma (OS) is the primary bone tumor in children and young adults.  Currently, there are no reliable, non-invasive biological markers to detect the presence or progression of disease, assess therapy response, or provide upfront prognostic insights. Using a qPCR-based platform that analyzes more than 750 miRNAs, we analyzed control and diseased-associated plasma from a genetically engineered mouse model of OS to identify a profile of four plasma miRNAs.

overall_design: Plasma from mice with OS were profiled for miRNAs and compared with the profile of plasma from disease-free mice

first: Jason

last: Yustein

first: Wendy

last: Allen-Rhoades


title: Lenti-miR Library SW620, Pre vs Post Intrahepatic Selection

status: Public on Jan 16 2015

city: New York

first: Jia Min

last: Loo

state: NY

address: 1230 York Avenue #342

institute: The Rockefeller University

summary: Cells were transduced with a lentiviral Lenti-miR library composed of 661 miRNAs (System Biosciences) at a low multiplicity of infection (MOI) such that each cell over-expressed a single miRNA. The transduced population was then injected intra-hepatically into NOD-SCID mice for in vivo selection of miRNAs that when over-expressed, either promoted or suppressed metastatic liver colonization. Genomic DNA PCR amplication and recovery of lenti-viral miRNA inserts was performed on cells prior to injection, and from liver nodules, according to the manufacturer’s protocol. miRNA array profiling allowed for miRNA insert quantification prior to and subsequent to in vivo selection.

overall_design: To use an unbiased approach to identify regulators of colon cancer metastasis, we transduced a population of colon cancer cells, SW620, with a lenti-miR library comprising of 661 human miRNAs, such that each individual cells over-express a single miRNA. The heterogenous population is then injected into the liver of immunodeficient mice. We theorized that cells over-expressing miRNAs that modulate colon cancer metastais will have differential representation in the whole population compared to a reference pool of cells. miRNAs that suppressed colon cancer metastasis will be lost in the resulting pool, while miRNAs that promote metastasis will be over-represented compared to the reference pool. Replicate pools of cells were transduced and injected into mice. After a period of 3-5 weeks, liver nodules were taken out and processed for lenti-viral derived miRNA profiling (Post samples) and compared to the reference pool of cells that were not injected into the mice (Pre Samples). The changes in miRNA representation between cells that underwent liver colonization were analyzed.

first: Jia

middle: M


title: Lenti-miR Library WiDR, Pre vs Post Intrahepatic Selection

overall_design: To use an unbiased approach to identify regulators of colon cancer metastasis, we transduced a population of colon cancer cells, WiDR, with a lenti-miR library comprising of 661 human miRNAs, such that each individual cells over-express a single miRNA. The heterogenous population is then injected into the liver of immunodeficient mice. We theorized that cells over-expressing miRNAs that modulate colon cancer metastais will have differential representation in the whole population compared to a reference pool of cells. miRNAs that suppressed colon cancer metastasis will be lost in the resulting pool, while miRNAs that promote metastasis will be over-represented compared to the reference pool. Replicate pools of cells were transduced and injected into mice. After a period of 3-5 weeks, liver nodules were taken out and processed for lenti-viral derived miRNA profiling (Post samples) and compared to the reference pool of cells that were not injected into the mice (Pre Samples). The changes in miRNA representation between cells that underwent liver colonization were analyzed.


title: Identification of Cardiovascular Lineage Descendants at Single Cell Resolution

city: Pittsburgh

first: Guang

last: Li

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

summary: The transcriptional profiles of cardiac cells derived from murine embryos and from mouse embryonic stem cells (mESCs) have primarily been studied within a cell population. However, the characterization of gene expression in these cells at a single cell level may demonstrate unique variations that are not able to be appreciated as a pool. In this study, we aimed to establish a single cell quantitative PCR platform and perform side-by-side comparison between cardiac progenitors cells (CPCs) and cardiomyocytes (CMs) derived from mESC and mouse embryos. We first generated a reference map for cardiovascular single cells through quantifying lineage-defining genes for CPCs, CMs, smooth muscle cells (SMCs), endothelial cells (EDCs), fibroblasts, and mESCs. This panel was then applied against day 10.5 embryonic heart single cells to demonstrate its ability to identify each endocardial cell and chamber-specific CM. In addition, we compared the gene expression profile of embryo- and mESC-derived CPCs and CMs at different developmental stages and showed that mESC-derived CM is phenotypically similar to embryo-derived CM up to the neonatal stage. Furthermore, we show that single cell expression assay coupled with time-lapse microscopy can resolve the identity and the lineage relationships between progenies of single cultured CPC. With this approach, we found differential propensity for mESC-derived CPCs to become SMCs or CMs, whereas single embryo-derived CPC to become either EDCs or CMs. These results demonstrate that multiplex gene expression analysis in single cells is a powerful tool in examining the unique behavior in individual embryo- or mESC-derived cardiac cells.

overall_design: Microfluidic-enabled single cell qPCR analysis of mESC- and embryo-derived cardiac cells.

first: Karolina

last: Plonowska

first: Rajarajan

last: Kuppusamy

first: Anthony

last: Sturzu

first: Sean

last: Wu


title: Comparison of in vivo collected oocytes from animals with high and low oocyte developmental potential (HOP, LOP) at both the immature and mature stage

status: Public on Jan 22 2015

city: Nouzilly

first: Rozenn

last: DALBIES-TRAN

address: Centre de Recherches INRA

country: France

institute: INRA

summary: Comparative transcriptomic analyses were performed at both the immature and at the mature stages between oocytes collected from cows with a high or low embryo development potential (HOP, LOP) as characterized by in vitro fertilization and embryo development.

overall_design: 1 biological replicate each from 3 HOP animals and 3 LOP animals, both at the immature stage and mature stage

last: Dalbies-Tran

first: Leslie

last: Angulo

first: Sylvain

last: Auclair

first: Christelle

last: Hennequet-Antier

first: Guyader-Joly

last: Catherine


title: Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis

status: Public on Jan 11 2015

city: Cologne

first: Julieta

last: Mateos

address: Carl-von-Linné-Weg 10

department: Department of Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

summary: The transition to flowering in plants is controlled by a regulatory network that responds to both developmental and environmental signals. The MADS-box genes FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) are major flowering repressors that enhance responses to environmental cues such as winter temperatures, high ambient temperatures and photoperiod. FLC and SVP physically interact in vivo and mutation of each gene causes early flowering while the double mutant is more extreme. The molecular mechanisms underlying these genetic interactions are mostly unknown. We addressed the regulatory input of these two key transcription factors (TFs) both individually and as a complex at the genome-wide level through ChIP-seq and microarray expression analysis in single and double mutants. Analysis of each TF demonstrated that the complex acts predominantly via functional redundancy in the repression of flowering. SVP and FLC bind to the same regions of the flowering genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FLOWERING LOCUS T (FT) but do not require the presence of the other to bind. However, genome-wide identification of SVP and FLC occupancy events revealed that their binding scenarios are quantitatively and qualitatively affected by the presence of the cognate partner. A subgroup of genes whose regulation by these TFs depends exclusively on combinatorial binding of both proteins was identified, demonstrating a qualitatively essential role of the SVP-FLC complex. Some of these genes are involved in the control of flowering through direct and indirect regulation of Gibberellin-related processes. Cis-regulatory elements enriched only at such complex-bound sites were identified. Thus the regulatory output mediated by SVP and FLC reveals substantial flexibility, leading to dependent and independent DNA binding that enables additive, cooperative and repressive modes of co-regulation.

overall_design: In total 48 samples; 24 leaf samples corresponding to two different growing conditions, 24 apex samples corresponding to two different growing conditions.

middle: L

first: Pedro

last: Madrigal

first: Kenichi

last: Tsuda

first: Vimal

last: Rawat

first: René

last: Richter

first: Maida

last: Romera-Branchat

first: Fabio

last: Fornara

first: Korbinian

last: Schneeberger

first: Paweł

last: Krajewski

first: George

last: Coupland


title: Gene copy analysis of the F1 haploid progeny generated by Hypocrea jecorina CBS999.97 sexual development

status: Public on Jan 07 2015

city: Taipei

first: Ting-Fang

last: Wang

address: Academia Sinica. 128 Sec. 2, Academia Rd

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary:
Array-based comparative genome hybridization.
H. jecorina undergoes a heterothallic reproductive cycle, and the mating yields asci with 16 linearly arranged ascospores. Here we have compared whole genome gene copy number in the F1 progeny.

overall_design: We determined genome-wide gene copy number in the genomes of ascospores generated from diploid wild-type strain

first: Chia-Ling

last: Chen

first: Yu-Chien

last: Chuang

first: Shu-Yu

last: Tung


title: Saccharomyces cerevisiae: DSB mapping by Break-chip in a two-color experiment (G1 control vs. S phase samples)

status: Public on Jan 12 2015

city: Syracuse

first: Wenyi

last: Feng

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

summary: Break-chip (microarray-based double strand break mapping) analysis of mec1 cells recovering from 200 mM hydroxyurea in the presence or absence of 0.8 micromolar bathophenanthroline sulfonate (BPS).

overall_design: We asked if the presence of an iron chelator, BPS, during cell recovery from transient exposure to 200 mM hydroxyurea changes the global patterns of DNA double strand breaks (DSBs).  We used a yeast checkpoint mutant, mec1, which has been shown to produce DSBs at replication forks after hydroxyurea was removed from the cell culture.  We synchronously released cells from the G1/S transition into S phase in the presence of 200 mM hydroxyurea.  After 1h treatment, the drug was removed and cells were allowed to recover in fresh medium for 1h in the presence or absence of 0.8 micromolar BPS.  Recover (R) samples, R-1h-BPS and R-1h+BPS, as well as the G1 control samples were collected. Break-chip analysis was performed as previously described (Feng et al., G3(Bethesda) 2011 Oct;1(5):327-35. doi: 10.1534/g3.111.000554).

first: Elizabeth

last: Hoffman


title: Genome instability of the segmentally aneuploidy progeny

summary: Array-based comparative genome hybridization. The aneuploid progeny could return to euploid state.

overall_design: We determined genome-wide gene copy number in the genomes of aneuploid progeny after 14, 24 and 34 days vegetative propagation in dextrose-containing rich medim.

first: Wan-Chen

last: Li

first: Paul

middle: W

last: Hsu


title: Genome-wide identification of Bacillus subtilis Zur-binding sites.

status: Public on Jan 06 2015

city: Jouy-en-Josas

first: Sandrine

last: Auger

address: INRA-Domaine de Vilvert

type: Genome binding/occupancy profiling by genome tiling array

summary:
The transcriptional factor Zur plays a key role in regulating zinc homeostasis in Bacillus subtilis.
The genomic sites bound by Zur were mapped using a chromatine immunoprecipitation approach. This allowed the identification of 80 inter- and intragenic chromosomal sites bound by Zur.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: This data set contains 2 samples. Immunoprecipitated (IP) DNA from Bacillus subtilis BSAS36 strain (BSB1, a tryptophan-prototrophic derivative 168 strain expressing a SPA-tagged Zur protein) were extracted from bacterial cells in the exponential growth phase. IP and whole-cell extract DNA were hybridized on tiling array to generate ChIP-on-chip profiles. Two biological replicates were anlyzed.

first: S

first: E

last: Prestel

first: P

last: Noirot


title: Whole genome tomato transcriptional response to Tetranychus urticae herbivory

status: Public on Jan 05 2015

first: Vladimir

last: Zhurov

state: ON

address: 1151 Richmond Street

department: Biology

country: Canada

institute: University of Western Ontario


title: Caspase-2-dependent tumor suppression does not depend on the scaffold protein Raidd

status: Public on Jan 14 2015

city: Innsbruck

first: Tatsiana

last: Aneichyk

state: - Please choose -

address: Innrain 80/82

department: Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

summary: The receptor-interacting protein-associated ICH-1/CED-3 homologous protein with a death domain (Raidd) functions as a dual adaptor protein due to its bipartite nature, and is therefore thought to be a constituent of different multiprotein complexes including the PIDDosome, where it connects the cell death-related protease, Caspase-2, with the p53-induced protein with a death domain 1 (Pidd1). As such, Raidd has been implicated in DNA-damage-induced apoptosis as well as in tumor suppression, the latter based on its role as a direct activator of Caspase-2, known to delay lymphomagenesis caused by overexpression of c-Myc or loss of ATM kinase. As loss of Caspase-2 leads to an acceleration of tumor onset in the Eµ-Myc mouse model we set out to interrogate the role of Raidd in this process in more detail. Our data obtained analyzing Eµ-Myc/Raidd-/- mice indicate that Raidd is unable to protect from c-MYC-driven lymphomagenesis. Similarly, we failed to observe an effect of Raidd-deficiency on thymic lymphomagenesis induced by y-irradiation or fibrosarcoma development driven by 3-methylcholanthrene. The role of Caspase-2 as a tumor suppressor can therefore be uncoupled from its ability to interact and auto-activate upon binding to Raidd. Further, we provide supportive evidence that the tumor suppressive role of Caspase-2 is related to maintaining genomic integrity and allowing efficient p53-mediated signaling. Overall, our findings suggest that Raidd, although described to be the key-adapter allowing activation of the tumor suppressor Caspase-2, fails to suppress tumorigenesis in vivo.

overall_design: Comparison of preB cells (Eµ-Myc transgene) lacking Raidd or Caspase-2 against wt cells.

first: L

last: Peintner

last: Dorstyn

last: Kumar

first: T

first: A

last: Villunger

first: C

last: Manzl


title: LPS induced Cytokines & Chemokines changes in E9.5 pregnant mouse uteri

status: Public on Jan 01 2015

city: Stanford

first: Hui

last: Zhao

state: California

address: 300 Pasture Drive

department: Pediatrics

institute: Stanford University

summary: Changes of Cytokines and chemokines profiles were sucessfully determined between mouse non-treated vs LPS treated pregnant uteri using Qiagen PCR array.

overall_design: Pregnant mouse (FVB strain E8.5-9.5) were treated with LPS(2.5ug/mouse) or saline as control. 8h- or 16-h later,  uteri tissues (N=3) were collected.


title: Expression data from Plasmodium falciparum schizonts

status: Public on Jan 13 2015

city: Boston

first: Matthias

last: Marti

state: MA

address: 665 Huntington Avenue

institute: Harvard School of Public Health

summary:
During intra-erythrocytic development, late asexually replicating Plasmodium falciparum parasites sequester from peripheral circulation. This facilitates chronic infection and is linked to severe disease and organ-specific pathology including cerebral and placental malaria. Immature gametocytes – sexual stage precursor cells – likewise disappear from circulation. Recent work has demonstrated that these sexual stage parasites are located in the hematopoietic system of the bone marrow before mature gametocytes are released into the blood stream to facilitate mosquito transmission. However, as sequestration occurs only in vivo and not during in vitro culture, the mechanisms by which it is regulated and enacted (particularly by the gametocyte stage) remain poorly understood.
We generated the most comprehensive P. falciparum functional gene network to date by integrating global transcriptional data from a large set of asexual and sexual in vitro samples, patient-derived in vivo samples, and a new set of in vitro samples profiling sexual commitment. We defined more than 250 functional modules (clusters) of genes that are co-expressed primarily during the intra-erythrocytic parasite cycle, including 35 during sexual commitment and gametocyte development. Comparing the in vivo and in vitro datasets allowed us, for the first time, to map the time point of asexual parasite sequestration in patients to 22 hours post invasion, confirming previous in vitro observations on the dynamics of host cell modification and cytoadherence. Moreover, we were able to define the properties of gametocyte sequestration, demonstrating the presence of two circulating gametocyte populations: gametocyte rings between 0 and ~30 hours post invasion and mature gametocytes after around 7 days post invasion.

platform_organism:
Plasmodium berghei
Plasmodium falciparum

overall_design: We used 164/TdTom, a transgenic parasite line expressing a red fluorescent protein reporter under a gametocyte-specific promoter to generate schizont samples. Schizonts were subsequently isolated from both the fluorescent and non-fluorescent population by FACS and prepared for microarray analysis. Two biological replicates were produced for both the fluorescent and the non-fluorescent samples.

first: Kathrin

last: Buchholz


title: ChIP-chip from five horse cells with CENP-A

city: Bologna

first: Stefania

last: Purgato

address: via Selmi 3

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

summary: In the present study we analyzed centromeric localization on chromosome 11 in different horses and results showed that each individual exhibits a different arrangement of CENP-A binding domains.

overall_design: Comparison of five horse fibroblast cells


title: Whole genome tomato transcriptional response to jasmonic acid treatment and Tetranychus urticae herbivory [def-1]

summary:
The two-spotted spider mite, Tetranychus urticae, is one of the most significant mite pests in agriculture that can feed on more than 1,100 plant hosts, including model plants Arabidopsis thaliana and tomato, Solanum lycopersicum. In order to refine the involvement of jasmonic acid (JA) in mite-induced responses, we analyzed transcriptional changes in tomato JA signaling mutant defenseless1 (def-1) upon JA treatment and spider mite herbivory.
We used microarray to assess global gene expression in Solanum lycopersicum def-1 cv. Castlemart upon jasmonic acid treatment and Tetranychus urticae attack.

overall_design: 1 month old def-1 tomato plants were subjected to Tetranychus urticae attack through application of 100 adult mites on a terminal leaflet of leaf 3 for 24 h or plants were sprayed with 1 mM jasmonic acid solution.

first: Catherine

last: Martel

first: Marie

last: Navarro

first: Manuel

last: Martinez

first: Marc

last: Cazaux

first: Philippe

first: Alain

last: Migeon

first: M

middle: E

last: Santamaria

first: Nicky

last: Wybouw

first: Isabel

last: Diaz

first: Thomas

last: Van Leeuwen

first: Maria

last: Navajas

first: Miodrag

last: Grbic

first: Vojislava


title: A Gene Expression-based Predictor of Fibroepithelial Lesions of the Breast

city: Barcelona

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

country: Spain

institute: VHIO

summary: Gene expression data of fibroepithelial lesions of the breast

overall_design: In the study presented here, a well-defined cohort of 138 breast samples were used to acquire expression profiles of a total of 105 unique genes

first: Prat

last: Aleix

first: Vidal

last: Maria


title: Regulation of cold-inducible gene expression by RCI1A

city: Madrid

first: Rafa

last: Catalá

address: C/Ramiro de Maeztu n9

department: Biotechnology

institute: Centro de Investigaciones Biologicas

summary: Characterization of RCI1A role in the control of the response to low temperature of cold induced genes.

sample_organism:
Arabidopsis
Arabidopsis thaliana

overall_design: Two-condition experiment, rci1a vs. WT plants. Biological replicates: 3 aclimated and 3 control replicates.

first: Rafael

first: Rosa

last: Lopez-Cobollo

first: Trinidad

last: Angosto

first: J

last: Alonso

last: Ecker

first: Mar

last: Castellano

first: Julio

last: Salinas


title: Chip-chip from Z138 MCL cell line with SOX11 antibody

first: Virginia

last: Amador

address: Rossello 153

institute: IDIBAPS

summary:
To determine the role of SOX11 in aggressive lymphoid neoplasm, we first investigated direct target genes of this transcription factor using chromatin immunoprecipitation and DNA microarrays (ChIP-chip) in MCL cell lines.
Analysis of the exact location of SOX11 binding elements showed that SOX11 interacts with DNA predominantly in the enhancer regions (in 40% of the enriched regions) and intron segments (in 33% of the enriched regions), suggesting that in these genes SOX11 may interact with the general transcriptional machinery and transcriptional co-regulators.

overall_design: comparison of Z138 vs JVM2 cells

last: Vegliante

first: Jara

last: Palomero


title: Generation 2.5 Antisense Oligonucleotides Targeting the Androgen Receptor and its Splice Variants Suppress Enzalutamide-Resistant Prostate Cancer Cell Growth

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

type: Genome variation profiling by genome tiling array

summary:
Enzalutamide (ENZ) is a potent androgen receptor (AR) antagonist with activity in castration-resistant prostate cancer (CRPC); however, progression to ENZ-resistant (ENZ-R) CRPC frequently occurs with rising serum PSA levels, implicating AR full length (ARFL) or variants (AR-Vs) in disease progression. To define functional roles of ARFL and AR-Vs in ENZ-R CRPC, we designed 3 antisense oligonucleotides (ASO) targeting exon 1, intron 1, and exon 8 in AR pre-mRNA to knockdown either ARFL alone, or ARFL plus AR-Vs, and examined their respective effects in LNCaP-derived ENZ-R, as well as M12 and 22Rv1, cells. ENZ-R LNCaP xenografts express high levels of both ARFL and AR-V7 compared to CRPC LNCaP xenografts. In particular, ARFL levels were ~20-fold higher than AR-V7. ENZ-R LNCaP sub-lines, derived by selection from the ENZ xenografts, also expressed uniformly high levels of ARFL and AR-V7 compared to CRPC LNCaP cells. In addition, both ARFL and AR-V7 are highly expressed in the nuclear fractions of ENZ-R-LNCaP. In ENZ-R LNCaP cells, knockdown of ARFL alone, or ARFL plus AR-Vs, similarly induced apoptosis, suppressed cell growth and AR-regulated gene expression in vitro, and delayed tumour growth in vivo. In 22Rv1 cells that are inherently resistant to ENZ, knockdown of both ARFL and AR-Vs more potently suppressed cell growth, AR transcriptional activity and AR-regulated gene expression than knockdown of ARFL alone. These data indicate the AR is an important driver of ENZ resistance, and while the contributions of ARFL and AR-Vs can vary across cell systems, ARFL is the key driver in the ENZ-R LNCaP model. AR targeting strategies against both ARFL and AR-Vs is a rational approach for AR-dependent CRPC.
CRPC and ENZ-R LNCaP xenografts were generated as described in: Gleave, M.E., et al., Serum prostate specific antigen levels in mice bearing human prostate LNCaP tumors are determined by tumor volume and endocrine and growth factors. Cancer Res, 1992. 52(6): p. 1598-605.

overall_design: 6 samples were analyzed: 2 control castrate-resistant prostate cancer cell line xenografts and 4 castrate-resistant prostate cancer cell line xenografts treated with Enzalutamide until resistance emerged. Samples were competitively hybridized against a male reference pool using Agilent aCGH arrays.

first: Yoshiaki

last: Yamamoto

first: Alexander

last: Wyatt

first: Martin

last: Gleave


title: Gene expression divergence in experimentally evolved Drosophila pseudoobscura females

city: Uppsala

first: Göran

last: Arnqvist

address: Norbyvägen 18D

department: Ecology and Genetics

country: Sweden

institute: Uppsala University

summary: We used experimentally evolved Drosophila pseudoobscura females, who have experienced either enforced monogamy or increased polyandry for 100 generations, to assess divergence in their transcriptomic response to both mating system variation and mating experience.

overall_design: Gene expression was measured from 5-days old females from two experimentally evolved lines (M=monogamous, P=elevated polyandrous). We measured gene expression of females from each of the two selection lines 24h-h after mating with either M or with P males, or as virgins. The same design was repeated for two replicate selection lines per treatment, and within each we obtained three independent biological replicates per treatment category.

first: Elina

last: Immonen

first: Rhonda

middle: R

last: Snook

first: Michael

middle: G

last: Ritchie


title: MiR-133b targets antiapoptotic genes and  enhances death receptor-induced apoptosis

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Despite the importance of microRNAs (miRs) for regulation of the delicate balance between cell proliferation and death, only scarce evidence is currently available on their specific involvement during death receptor (DR)-mediated apoptosis. Transfection of mature miR-133b into resistant HeLa cells rendered these sensitive to tumor necrosis factor-alpha (TNFα)-induced cell death. Similarly, miR-133b treatment resulted in exacerbated proapoptotic responses to TNF-related apoptosis-inducing ligand (TRAIL) or an activating antibody to CD95 (Fas/APO1). Comprehensive analysis, encompassing global RNA and protein expression profiling performed by microarray experiments and pulsed stable isotope labeling by amino acids in cell culture (pSILAC), led to the discovery of the antiapoptotic proteins Fas apoptosis inhibitory molecule (FAIM) and glutathione-S-transferase pi (GSTP-1) as immediate miR-133b targets. In-vivo, expression of miR-133b in tumor specimens of prostate cancer patients could be proven as significantly downregulated in 75% of the cases, when compared with matched healthy tissue. Furthermore, introduction of synthetic miR-133b into an ex-vivo model of prostate cancer resulted in impaired proliferation and cellular metabolic activity. These results reveal the ability of a single miR to influence major apoptosis pathways, suggesting an essential role for this molecule during the process of cellular transformation, tumor generation and tissue homeostasis.

overall_design: Microarray experiments were performed as dual-color hybridizations. To compensate for dye-specific effects, a dye-reversal color-swap was applied

first: Juan

last: Patron

first: Stefan

middle: H

last: Kaufmann

first: Jörg

last: Schreiber

first: Monika

last: Jung

first: Klaus


title: Transcriptome analysis of Atino80-5 mutant in comparison with wild type.

status: Public on Dec 31 2014

city: Shanghai

first: Yan

last: Zhu

address: 2005, Songhu Road

department: Biochemistry

country: China

institute: Fudan University, School of life sciences

summary: INO80 is a conserved chromatin remodeler through evolution. We identified a novel ino80 mutant allele, Atino80-5, in Arabidopsis thaliana, and performed the transcriptome analysis of this mutant in comparison with wild type (WT).

overall_design: 12-day-old seedlings of wild-type (WT) and Atino80-5 mutant grown under standard growth condition were used for RNA extraction and microarray.


title: miRNA expression in developmental spinal cord

city: Baoshan

first: Botao

last: Zhao

state: Shanghai

address: 333 Nanchen Rd

department: college of life science

institute: Shanghai University

summary: This study compared the microRNA expression in mouse fetal spinal cord at day 13.5 and newborn mouse spinal cord.

overall_design: Three biological replications of the two samples were pooled. For each pooled sample, two technical replications were performed.

first: Youxin

last: Jin


title: Effect of Antigen, Type I IFN and STING Signaling on CD8 T Cell Immunity With Adenoviral Vaccines

status: Public on Dec 30 2014

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

summary: Recombinant adenoviral vectors (rAds), derived from distinct species with different serotypes, are lead vaccine candidates against Ebola, HIV, Tuberculosis and Malaria based on their potent induction of T cell immunity in humans. Importantly, rAds vary in their ability to induce protective cellular immunity. Here, the in vivo mechanisms controlling potency of CD8 T cell responses were assessed after vaccination with human-, chimpanzee- and simian-derived rAds encoding SIV-Gag. After rAd vaccination, we quantified antigen (Ag) expression and performed expression profiling of innate immune response genes in the draining lymph node. The most potent rAds (human-derived rAd5 and chimpanzee-derived chAd3) induced high and persistent Ag expression with low innate gene activation, while the less potent rAds exhibited reduced Ag expression with robust innate gene activation associated primarily with interferon (IFN) signaling. Abrogation of type I IFN or stimulator of IFN genes (STING) signaling increased Ag expression and accelerated CD8 T cell response kinetics, but did not alter memory responses or protection. Thus, the magnitude of memory CD8 T cell immune responses induced by rAds correlates with Ag expression but is independent of IFN and STING. These findings provide criteria for optimal induction of protective CD8 T cell immunity with rAd vaccines.

overall_design: Each microarray comes from an RNA sample obtained from a unique mouse.  There were no repeated RNA samples obtained from any mouse.  207 arrays were run overall, 189 from dLN and 18 from PBMCs obtained from mice vaccinated with different rAd vectors. The dLN arrays were run in three batches, denoted A-C, and the PBMCs were run in Batch D. Batch A (108 arrays)consisted of six biological replicates at each of three time points (8, 24 and 72 hours) post-vaccination with PBS, rAd5 (1 x 10^8 PU), rAd28 (1 x 10^8 PU), rAd35 (1 x 10^9 PU), sAd11 (1 x 10^8 PU) and sAd16 (1 x 10^8 PU). Batch B (46 arrays) consisted of four biological replicates at each of three time points (8, 24 and 72 hours) post-vaccination with chAd3 (1 x 10^8 PU), chAd63 (1 x 10^8 PU) and Poly I:C. Batch B also consisted of two biological replicates at each of three time points (8, 24 and 72 hours) post-vaccination with rAd5 (1 x 10^8 PU) and four biological replicates at each 8 hour time point post-vaccination with PBS (control). Batch C (35 arrays) consisted of five biological replicates at each 8 hour time point post-vaccination of WT, IFNabR-/- and STING gt/gt mice with PBS and chAd63 (3 x 10^7 PU). Batch C also consisted of five biological replicates at each 8 hour time point post-vaccination with rAd5 (3 x 10^7 PU). Batch D (18 arrays) consisted of the PBMC microarray set, which included six biological replicates at each 24 hour time point post-vaccination with PBS, rAd5 and rAd28.

first: Kylie

last: Quinn

first: Robert

last: Seder

first: Alan

last: Aderem


title: Mycobacterium tuberculosis: Cas9 Induced Vs uninduced cultures [Day 7]

status: Public on Dec 13 2014

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

country: India

institute: Translational Health Science and Technology Institute

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv::pTetInt-dcas9 comparing 100ng/ml ATc treated cells with Atc-untreated cells after 7 days of treatment with shaking at 200rpm at 37°C.

overall_design: Two-condition experiment, Cas9-induced (Test) Vs Cas9-uninduced cells (Control). Biological replicates: 1 test, 1 control. Three replicates per array.

first: Eira

last: Choudhary

first: Preeti

last: Thakur

first: Madhu

last: Pareek


title: Mycobacterium tuberculosis: Cas9 Induced Vs uninduced cultures [Day 4]

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv::pTetInt-dcas9 comparing 100ng/ml ATc treated cells with Atc-untreated cells after 4 days of treatment with shaking at 200rpm at 37°C.


title: Mycobacterium tuberculosis: Cas9 Induced Vs uninduced cultures

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

overall_design: Refer to individual Series


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

status: Public on Dec 27 2014

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: Microplastics represent a growing environmental concern for the oceans due to their potential capability to adsorb different classes of pollutants, thus representing a still unexplored source of exposure for aquatic organisms.  In this study polystyrene (PS) microplastics were characterized for their capability to adsorb pyrene (PYR) as model compound for polycyclic aromatic hydrocarbons, and transfer this chemical to filter feeding mussels Mytilus galloprovincialis.  Gene expression analyses of Mytilus galloprovincialis exposed to polystyrene (PS) microplastics and to polystyrene contaminated with pyrene (PS-PYR) have been performed trough a DNA microarray platform.

overall_design: For the exposure of mussels to microplastics, specimens of 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 and 18± 1 °C, salinity at 28–30 ‰. Contaminated plastics were prepared by maintaining a solution of <100µm microplastics (20g/L) with pyrene (50µg/L) in rotating conditions for 6 days. A total of 150 organisms were distributed into fifteen 6L- glass-beakers and exposed to virgin or contaminated plastics for 7 days: three replicates were performed for each of 3 treatments; Control (CNTR), Polystyrene (PS), Pyrene-treated Polystyrene (PS-PYR).Water was changed daily and both virgin and pyrene-treated particles re-dosed at a nominal concentration of 1.5 g/L. Four independent digestive glands pools for CNTR, PS and PS-PYR groups, each consisting of three individuals, were constituted for each treatment to perform DNA microarray analysis. Due to technical problems during the hybridization step, one pool belonging to PS group has been excluded by the dataset used for gene expression analyses. Gene transcription analyses of 12 digestive glands pools (four pools for each treatment composed by 3 digestive glands; CNTR, PS and PS-PYR) were performed using an 8X60K Agilent oligo-DNA microarray platform. 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: Milan

last: Massimo

first: Bargelloni

last: Luca

first: Pauletto

last: Marianna

first: Regoli

last: Francesco


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

city: Stockholm

first: Anna

last: Krook

address: von Eulers väg 4a

institute: Karolinska Institutet

summary:
The purpose of this study was to determine the miRNA expression profile of in vitro differentiation of human skeletal muscle cells and to couple changes in individual miRNA expression to transcriptional output of target genes.
miRNA expression profiling at six different time points during the in vitro differentiation process of human skeletal muscle cells from six subjects. RNA was harvested from myoblasts before induction of differentiation and at every other day for 10 following days.

overall_design: Temporal, time-course design with paired analysis (6 subjects). Biological replicates: 6 at day 0, 6 at day 2, 6 at day 4, 6 at day 6, 6 at day 8, and 5 at day 10. One replicate vs common reference RNA pool per array.


title: Thorax transcriptome from control and PABPN1-17ala-expressing flies

status: Public on Dec 12 2014

city: Paris

first: Capucine

last: TROLLET

address: GH Pitie Salpetriere Bat Babinski 47 bd de l'hopital

institute: Myology Research Center UMRS974 INSERM

summary:
Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset syndrome characterized by progressive degeneration of particular muscles. OPMD is caused by short GCG repeat expansions within the gene encoding the nuclear poly(A)-binding protein 1 (PABPN1) that extend an N-terminal polyalanine tract in the protein. Mutant PABPN1 aggregates as nuclear inclusions in OMPD patient muscles. We have created a Drosophila model of OPMD that recapitulates the features of the human disorder: progressive muscle degeneration, with muscle defects proportional to the number of alanines in the tract, and formation of PABPN1 nuclear inclusions. Wild-type human PABPN1 contains a stretch of 10 alanines following the initial methionine, which is expanded to 12–17 alanines in OPMD patients. In Drosophila, the PABPN1 homolog is the poly(A)-binding protein 2 (PABP2), which has the same function as PABPN1 in nuclear polyadenylation but lacks a polyalanine tract at the N-terminus. We used the UAS/Gal4 system to express mammalian PABPN1 in Drosophila. An alanine-expanded PABPN1 cDNA (encoding the 17 alanine tract) was cloned downstream of UAS sequences (UAS-PABPN1). Transgenic lines containing this construct were crossed to a Mhc-Gal4 driver, leading to muscle-specific expression. To gain insight into the molecular and physiological defects in OPMD we performed a transcriptomic analysis in OPMD fly muscles. Using microarrays, thorax gene expression was compared between control flies (Mhc-Gal4/+) and flies expressing PABPN1-17ala in thoracic muscles (UAS-PABPN1-17ala/+; Mhc-Gal4/+), at three time points (days 2, 6 and 11).
Transcriptome of thorax RNA samples from control (Mhc-Gal4/+) flies and flies expressing PABPN1-17ala (UAS-PABPN1-17ala/+; Mhc-Gal4/+)

overall_design: Total RNA was isolated from 50 adult thoraxes per genotype (WT=Mhc-Gal4/+ and OPMD=UAS-PABPN1-17ala/+; Mhc-Gal4/+), per time-point (day 2, 6 and 11), in triplicates.

first: Martine

last: Simonelig

first: Aymeric

last: Chartier

first: Ellen

last: Sterrenburg

first: Verez

last: Raz

first: Silvère

last: van der Maarel


title: Differential MicroRNAs in Microarray profile of Retinoblastoma in EpCAM silenced Y 79 cells

status: Public on Dec 01 2014

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: We aimed to identify microRNAs which are altered upon EpCAM silencing.EpCAM is over expressed molecule in Retinoblastoma. Retinoblastoma Y 79 cell line was used as model to study the differential expression of microRNA in EpCAM siRNA treated cells.To validate technique we further confirmed deregulated expression of few microRNAs in Y 79 cells using Real Time PCR technique.

overall_design: Agilent one-color experiment,Organism: Homo sapiens ,Agilent Human miRNA 8x15k Arrays AMADID: 029297

last: Beta

first: Subramanian

last: Krishnakumar


title: Response to different N-acyl homoserine lactones and N-acyl homoserine lactones-pretreated plants to secondary challenge with flg22.

status: Public on Nov 26 2014

city: Giessen

first: Adam

last: Schikora

address: Heinrich-Buff-Ring 26-32

department: IPAZ

institute: JLU Giessen

summary: In order to gain coherent insights into plant responses we performed transcriptional analysis of Arabidopsis seedling after treatment with three different AHLs: N-hexanoyl-L-homoserine lactone (C6-HSL), N-3-oxo-decanoyl-L-homoserine lactone (oxo-C10-HSL), and N-3-oxo-tetradecanoyl-L-homoserine lactone (oxo-C14-HSL).  Furthermore, we analyzed the transcriptome of oxo-C14-HSL pretreated plants after a secondary challenge with 100 nM flg22 for 2 and 24 hours after treatment.

overall_design: Gene expression in Arabidopsis thaliana seedlings were measured after a 3-days-pretreatment with 6 µM of three different N-acyl homoserine lactones in comparison to plants treated with the coresponding volume of acetone (solvent control). Plants pretreated with oxo-C14-HSL were in addition treated with 100nM of flg22 to induced defense response. Three independent experiments were performed (replicates).

first: Sebastian

middle: T

last: Schenk

first: Birgit

last: Samans


title: Quantitative modeling of transcription factor binding specificities using DNA shape

status: Public on Nov 04 2014

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

type: Genome binding/occupancy profiling by array

summary: Accurate predictions of the DNA binding specificities of transcription factors (TFs) are necessary for understanding gene regulatory mechanisms. Traditionally, predictive models are built based on nucleotide sequence features. Here, we employed three- dimensional DNA shape information obtained on a high-throughput basis to integrate intuitive DNA structural features into the modeling of TF binding specificities using support vector regression. We performed quantitative predictions of DNA binding specificities, using the DREAM5 dataset for 65 mouse TFs and genomic-context protein binding microarray data for three human basic helix-loop-helix TFs. DNA shape-augmented models compared favorably with sequence-based models for these predictions. Although both k-mer and DNA shape features encoded the interdependencies between nucleotide positions of the binding site, using DNA shape features reduced the dimensionality of the feature space compared to k-mer use. Finally, analyzing the weights of DNA shape-augmented models uncovered TF family- specific structural readout mechanisms that were not obvious from the nucleotide sequence.

overall_design: Three genomic-context protein binding microarray (gcPBM) experiments of human transcription factors were performed. Briefly, the gcPBMs involved binding his-tagged transcription factors c-Myc, Max, and Mad1(Mxd1) to double-stranded 180K Agilent microarrays in order to determine their binding specificity for putative DNA binding sites in native genomic context. Briefly, we represent three categories of 36-bp sequences: 1) bound probes, 2) unbound probes (or negative controls), and 3) test probes. Bound probes corresponded to genomic regions bound in vivo by c-Myc, Max, or Mad2 (ChIP-seq P < 10^(-10) in HeLaS3 or K562 celld (ENCODE)) that contain at least two consecutive 8-mers with universal PBM E-score > 0.4 (Munteanu and Gordan, LNCS 2013). All putative binding sites occur at the same position within the probes on the array. “Unbound” probes corresponded to genomic regions with ChIP-seq P < 10^(-10) and a maximum 8-mer E-score < 0.2. We also designed test probes that contain, within constant flanking regions, all nnCACGTGnn 10-mers and 18 nnnCACGTGnnn 12-mers (where n = A, C, G, or T). Each DNA sequence represented on the array is present in 6 replicate spots. We report the gcPBM signal intensity for each spot. The PBM protocol is described in Berger et al., Nature Biotechnology 2006 (PMID 16998473).


title: The ThbZIP1 can be regulated by an ABF Transcription Factor and sensitivity to ABA treatment

status: Public on Nov 01 2014

city: Urumqi

first: Xiaoyu

last: Ji

address: Beijing road

institute: Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences

summary: In the current report, we report that ThbZIP1 is a direct target gene of the ThABF1 transcription factor. There are three ABRE motifs in the promoter of ThbZIP1, Yeast one-hybrid (Y1H) assays showed that a ABF protein, ThABF1, specifically binds to the ABRE motifs. The interaction between ThABF1 and the promoter of ThbZIP1 was further confirmed by transient expression assays in tobacco leaves. Chromatin Immunoprecipitation (ChIP) results suggested that binding of ThABF1 to ABRE motifs in the promoter of ThbZIP1 occurs in vivo in Tamarix hispida to regulate the expression of ThbZIP1. Moreover, ThABF1 and ThbZIP1 share similar expression patterns in response to salt, drought, ABA, methyl viologen (MV) and cold stress. Microarray analyses results showed there were 1,662 and 1,609 genes that were significantly upregulated or downregulated, respectively, under ABA stress conditions. ThbZIP1 regulated the genes via binding to the C-, G- or A-box motifs in their promoter sequences. Based on these data, the results suggested a regulatory network model mediated by ThbZIP1, under abiotic stress conditions, ThABF1 regulates the expression of ThbZIP1, and the activated ThbZIP1 binds to bZIP recognition sequences or other motifs to regulate the expression of genes containing these motifs in their promoters.

overall_design: Differentially expression genes of ThbZIP1-overexpression plants and wild type of Columbia Arabidopsis thaliana were measured under ABA stressed and normal condition for 3 hours, respectively. Two independent experiments were performed at each treatment using different plants for each experiment.

first: Yucheng

last: Wang


title: A novel capsule-mediated virulence mechanism in a bacterial pathogen

status: Public on Oct 07 2014

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

institute: Institut Pasteur de Lille

summary: Bordetella pertussis, the causative agent of whooping cough, produces a microcapsule at its surface but its role in pertussis pathogenesis remained to be investigated.Absence of KpsT, a membrane-associated protein involved in the polysaccharide transport resulted in the down-modulation of a large number of virulence genes which correlated with strong attenuation in vivo.

overall_design: One condition experiment, DeltaKpsT against WT. Biological replicates: 3 control replicates, 3 mutants replicates.

first: Regina

last: Hoo

first: Ludovic

last: Huot

first: Sylvie

last: Alonso


title: A comparison of genome-wide DNA methylation patterns between different tissues from patients with coronary heart disease

status: Public on Oct 31 2014

city: Tomsk

first: Anton

middle: Vladimirovich

last: Markov

state: Tomskaya oblast

address: Nab. Ushaiki, 10

country: Russia

institute: Research Institute of Medical Genetics

summary: Using the Illumina Infinium Human Methylation27 BeadChip, we performed a genome-wide analysis of DNA methylation in right coronary artery in the area of advanced atherosclerotic plaques, atherosclerotic-resistant internal mammary arteries, and great saphenous veins obtained from same patients with coronary heart disease. The resulting DNA methylation patterns were markedly different between all the vascular tissues. The genes hypomethylated in athero-prone arteries to compare with atherosclerotic-resistant arteries were predominately involved in regulation of inflammation and immune processes, as well as development. The great saphenous veins exhibited an increase of the DNA methylation age in comparison to the internal mammary arteries. Gene ontology analysis for genes harboring hypermethylated CpG-sites in veins revealed the enrichment for biological processes associated with the development. Four CpG-sites located within the MIR10B gene sequence and about 1 Kb upstream of the HOXD4 gene were also confirmed as hypomethylated in the independent dataset of right coronary arteries in the area of advanced atherosclerotic plaques in comparison with the other vascular tissues.

overall_design: Bisulfite converted genomic DNA from 24 samples was denatured, whole-genome amplified, fragmented and subsequently hybridized to the Illumina Infinium 27k Human Methylation Beadchip.

first: Maria

last: Nazarenko

middle: V

first: Igor

middle: N

last: Lebedev

first: Maxim

middle: B

last: Freidin

first: Aleksei

last: Sleptcov

first: Iuliya

last: Koroleva

last: Frolov

first: Vadim

last: Popov

first: Olga

last: Barbarash

first: Valery

last: Puzyrev


title: Array-CGH and Next-generation sequencing of duplication CNVs reveals that most are tandem and some disrupt genes at breakpoints

status: Public on Oct 25 2014

city: Atlanta

first: Karen

last: Hermetz

state: GA

address: 1518 Clifton Rd

department: Human Genetics

institute: Emory University School of Medicine

summary: Interpreting the genomic and phenotypic consequences of copy number variation (CNV) is essential to understand the etiology of genetic disorders. Whereas deletion CNVs obviously lead to haploinsufficiency, duplications may cause disease through triplosensitivity, gene disruption, or gene fusion at breakpoints. The mutational spectrum of duplications has been studied at certain loci and in some cases these copy number gains are complex chromosome rearrangements involving triplications and/or inversions. However, the organization of clinically relevant duplications throughout the genome has not been investigated on a large scale. Here, we fine mapped 184 germline duplications (14.7 kb-25.3 Mb; median 532 kb) ascertained from individuals referred for diagnostic cytogenetics testing. We performed next-generation sequencing (NGS) and whole-genome sequencing (WGS) to sequence 130 breakpoints from 112 subjects with 119 CNVs and found that most (83%) were tandem duplications in direct orientation. The remainder were triplications embedded within duplications (8.4%), adjacent duplications (4.2%), insertional translocations (2.5%), or other complex rearrangements (1.7%). In addition, we predicted six in-frame fusion genes at sequenced duplication breakpoints. Four gene fusions were formed by tandem duplications, one by two interconnected duplications, and one by duplication inserted at another locus. These novel fusion genes could be related to clinical phenotypes and warrant further study. Though most duplications are positioned head-to-tail adjacent to the original locus, those that are inverted, triplicated, or inserted can disrupt or fuse genes in a manner that may not be predicted by conventional copy number analysis. Thus, interpreting the genetic consequences of duplication CNVs requires breakpoint-level analysis.

overall_design: High resolution array CGH; two-color experiment, clinical patient vs. normal control gDNA; sex mis-matched

first: Brooke

last: Weckselblatt

first: Scott

last: Newman

first: M

middle: K

last: Rudd


title: Gene expression profiling of 151 pediatric low-grade gliomas

status: Public on Aug 29 2014

city: Boston

first: Rameen

last: Beroukhim

address: 450 Brookline Av

department: Cancer Biology

institute: DANA-FARBER CANCER INSTITUTE

summary:
We performed gene expression profiling on 151 paraffin-embedded PLGGs from different locations, ages, histological subtypes as well as BRAF genetic status
We also compared molecular differences to normal pediatric brain expression profiles to observe whether those patterns were mirrored in normal brain expression.

overall_design:
We analyzed the expression of 6,100 genes among 151 FFPE pediatric and 15 FFPE adult low-grade gliomas and analyzed how the expression patterns changes with location, age, histology and BRAF genomic status and how those differences were mirrored in normal brain expression.
The values in the sample 'characteristics' columns represent;
Location; SUP= Supratentorial, INF= Infratentorial
Histology; PA= pilocytic astrocytoma, GG= ganglioglioma, DNT= dysembryoplastic neuroepithelial tumor, OD= oligodendroglial tumors, NOS= not otherwise specified tumors
BRAF status; DUP= BRAF duplication, MUT= BRAF V600E mutation, WT= wild type, ND= not determined
Primary or recurrent tumor; P=primary, R=recurrent
Primary tumor that further progressed; 1=yes, 0=no, _=recurrent tumors only

first: Guillaume

last: Bergthold

first: Pratiti

last: Bandopadhayay

first: Mark

last: Kieran

first: Jennifer

middle: A

last: Chan


title: Real-time quantitative PCR analysis of human adipose derived stem cells microvesicles

status: Public on Aug 08 2014

first: Dong

last: Liu

address: 720 Westview Drive, SW

department: Cardiovascular Research Institute

institute: Morehouse School of Medicine

summary: ASC was preconditioned with endothelial differentiation medium for 4 days; after which the medium was changed to endothelial basal medium (2% FBS-MV Free) for two days; The conditioned medium was then harvested for microvesicle isolation; The ASC-MV were used for microarray analysis

overall_design: qPCR gene expression profiling; ASC-MV were used in duplicate

first: Ting

last: Kang

first: Tia

last: Jones


title: Arabidopsis AtbHLH112 protein positively regulates tolerance to abiotic stress and binds to the E-box and a novel motif GCG-box

status: Public on Aug 09 2014

city: Harbin

first: Yujia

state: Heilongjiang

address: 1 Xuehai Street

institute: Harbin University of Commerce

summary: Plant basic helix-loop-helix (bHLH) transcription factors are involved in physiological and developmental processes, and also play essential roles in abiotic stresses. However, their exact roles in abiotic stress are still need to be elucidated, and most of bHLHs have not been functionally characterized. In the present study, we characterized the functional role of AtbHLH112 in response to abiotic stresses. AtbHLH112 is a nuclear-localized protein, and its nuclear-localization is induced by salt, drought and ABA. Besides binding to E-box motif, AtbHLH112 is found to bind to a novel motif with the sequence “GG[GT]CC[GT][GA][TA]C” (GCG-box), and the binding affinity is induced by salt and ABA. Gain- and loss-of-function analyses showed that the transcript level of AtbHLH112 is positively correlated with salt and drought tolerance. AtbHLH112 mediates stress tolerance by upregulating the expression of P5CS genes and decreasing the expression of P5CDH and PRODH genes to increase proline levels, and via enhancing the expression of POD and SOD genes to improve ROS scavenging ability. All data together suggested that AtbHLH112 regulates the expression of genes through binding to GCG-box and E-box to mediate the physiological stress responses, including proline biosynthesis and ROS scavenging pathways to enhance stress tolerance.

overall_design: Differentially expression genes of AtbHLH112-overexpression plants, mutant (SALK_033618C) plants and wild type of Columbia Arabidopsis thaliana were measured under salt stressed and normal condition for 3 hours, respectively. Three independent experiments were performed at each treatment using different plants for each experiment.

first: Yucheng

last: Wang


title: Effect of TLR Ligation on the Differentiation and Function of Human mMDSC

status: Public on Jul 21 2014

city: Frederick

first: Dennis

last: Klinman

state: Maryland

address: 1050 Boyles St

department: Cancer and Inflammation Program

institute: National Institutes of Health

summary: Immunosuppressive microenvironments block the activity of tumoricidal T and NK cells, allowing cancers to avoid immune elimination.  Monocytic myeloid-derived suppressor cells (mMDSC) are an important component of these immunosuppressive milieus.  Human mMDSC respond to stimulation via their Toll-like receptors by differentiating into macrophage.  Agonists targeting TLRs 1/2 (such as PAM3) induce mMDSC to mature into immumosuppressive M2-like macrophage through a process that involves TNF and IL6.  Agonists targeting TLRs 7/8 (such as R848) cause the same precursors to mature into tumoricidal M1-like macrophages, a process in which IL12 plays a central role.  The immune suppression mediated by mMDSC is reversed by exposure to TLR 7/8 agonists which thus might be useful adjuncts for tumor immunotherapy.

overall_design: In this study we looked at several time points. hMDSC from four different donors were sorted from PBMC then cultured in the presence of R848, Pam 3 or left unstimulated for 30, 75 and 225 minutes.   Late time points included samples from seven donors after 3 days in culture with the same TLR ligands.   For microarray experiments total RNA was extracted, amplified into aRNA and coupled to Cy5.  Similarly amplified RNA from universal RNA was coupled to Cy3 and used as a reference for each array.

first: Jing

first: Yuko

last: Shirota

first: Hidekazu

first: Debra

last: Tross


title: C. albicans biofilm development

status: Public on Oct 01 2014

city: San Francisco

first: Emily

middle: Patricia

last: Fox

state: CA

address: 600 16th Street, GH - N374

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary: Transcriptional profiling of C. albicans in biofilms after 90 min of adherence or 8 h, 24 h, or 48 h of development; compared to C. albicans in suspension cultures grown to log at 30 deg or 37 deg or grown to stationary phase at 30 deg or collected from the unadhered cells in the biofilm assay.

overall_design: At least 2 biological replicates for each condition. All experiments are multiple condition: C. albicans in particular growth condition vs. mixed reference of all conditions in that experiment.

middle: P


title: Effects of caffeine ingestion in Drosophila melanogaster male thorax and abdomen.

status: Public on Jul 04 2014

city: dijon

first: Stéphane

last: Fraichard

state: Please select...

address: 6 bd gabriel

institute: csga UMR 6265 CNRS INRA  Université de Bourgogne

summary: To screen for xenobiotic-metabolizing-enzyme genes (XME) induced by caffeine exposure, a microarray experiment (performed with a Drosophila pangenomic array (Agilent 4 X 44K) was carried out between control and individuals exposed to caffeine (18mM ). Among 23401 genes consistantly found in the three biological replicates, 13108 showed a significant variation. 749 genes were over-expressed whereas 1518 were under-expressed. Interestingly, several genes belonging to all major classes of detoxification enzymes including XME were among the most highly induced such as CYP12d1, CYP6a8 and CYP6d5.

overall_design: Caffeine ingestion induced gene expression in Drosophila melanogaster male thorax and abdomen was mesured at 12h after exposure to doses of 0, 18mM of caffeine. Three independant experiments were performed at each dose using different drosophila for each experiment.

first: Alexandra

last: Coelho

first: Jean-Marie

last: Heydel


title: Widespread Discordance of DNA Methylation Between two Accessible Human Tissues

status: Public on May 31 2014

city: Vancouver

first: Michael

middle: S.

last: Kobor

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: Inter-individual variability in DNA methylation has been hypothesized to contribute to complex phenotypes through epigenetic modulation of gene expression levels. Population epigenetic studies have been examining differences in DNA methylation in a variety of accessible tissues for association with specific diseases or exposures, but relatively little is known about how this inter-individual variation differs between tissues. This study presents an analysis of global DNA methylation differences between matched peripheral blood mononuclear cells and buccal epithelial cells; specifically it examines differential DNA methylation, probe-wise DNA methylation variance, and how methylation relates to a number of demographic factors across the two tissues. We found that peripheral blood mononuclear cells have overall higher DNA methylation than buccal epithelial cells, and regions of the genome that are differently methylated between the tissues tend to have low CpG density. We also discovered that although both tissues show extensive probe-wise variability, the specific regions and magnitude of variability differed between tissues. Finally, we observed that while both buccal epithelial and peripheral mononuclear blood cell DNA methylation was associated with gender, only  methylation of the latter was associated with body mass index. The work presented here offers insight into variability of DNA methylation between individuals and across tissues and the suitability of buccal epithelial and peripheral mononuclear cells for the biological questions explored by epigenome-wide association studies in human populations.

overall_design: This cohort consist of genomic DNA extracted from the peripheral blood mononuclear cells and buccal epithelial cells of 25 individuals, bisulphite converted and hybridized to the Illumina GoldenGate Methylation Cancer Panel for genome wide DNA methylation profiling

first: Ruiwei

last: Jiang

first: Meaghan

middle: J

first: Edith

last: Chen

first: Sarah

middle: M

last: Neumann

first: Hunter

last: Fraser

first: Gregory

last: Miller

middle: S


title: Fetal-Adult Cardiac Transcriptome Analysis in Rats with Contrasting Left Ventricular Mass Reveals New Candidates for Cardiac Hypertrophy

status: Public on Jul 01 2014

city: Münster

first: Mona

last: Riemenschneider

address: Domagkstraße 3

institute: Genetic Epidemiology, University of Muenster

summary: Reactivation of fetal gene expression patterns has been demonstrated to play a crucial role in common cardiac diseases in adult life including left ventricular (LV) hypertrophy (LVH). Thus, increased wall stress and neurohumoral activation are discussed to induce the return to expression of fetal genes after birth in LVH. We therefore aimed to test whether fetal gene expression programs are linked to the genetic predisposition to LVH. We performed genome-wide gene expression analysis by microarray-technology in a genetic rat model of LVH, i.e. the stroke-prone spontaneously hypertensive rat (SHRSP), to identify differences in expression patterns between day 20 of development (E20) and week 14 in comparison to a normotensive rat strain with low LV mass, i.e. Fischer (F344). 15232 probes from LV RNA from rats at week 14 and at E20 were detected as expressed (p < 0.05) and screened for differential expression. We identified 24 genes with a SHRSP specific up-regulation and 21 genes up-regulated in F344. Further bioinformatic analysis presented Efcab6, Ephx2 and Kcne1 as candidate genes for LVH that showed only in the hypertensive SHRSP rat a differential expression pattern during development and were significantly differentially expressed in adult SHRSP rats compared with two F344 and normotensive Wistar-Kyoto rats. They represent thus interesting novel targets for further functional analyses and the elucidation of mechanisms leading to LVH. Here we report a new approach to identify candidate genes for cardiac hypertrophy by analysing both gene expression differences between strains with contrasting cardiac phenotype and additionally the gene expression program during development.

overall_design: 26 samples for analysis; no replicates

first: Katja

last: Graboswki

first: Leonard

last: Schulte

first: Annika

last: Witten

first: Angela

last: Schulz

first: Monika

last: Stoll

first: Reinhold

last: Kreutz


title: The microbial functional structure along an elevation gradient of the Shennongjia Mountain as characterized by GeoChip

status: Public on Jun 13 2014

city: Beijing

first: Junjun

last: Ding

address: Haidian

institute: Tsinghua University

summary: Known as “The Oriental Botanic Garden” and the natural gene bank of biological species, Shennongjia is one of the most biologically diverse areas in China and a member of UNESCO's World Network of Biosphere Reserves. The macro-organism resources of shennongjia have been deeply explored. However, the microbial community structure was scarcely detected. In this study, we aim to detedect the microbial community along six sites of Shennonajia Mountain and explore the major controlling factor in shaping microbial community with a microarray-based metagenomics tool named GeoChip 4.2.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Seventy-three samples were collected from six sites along the Shennongjia Mountain, with 5-15 replicates in every site

first: Yunfeng

last: Yang

first: Yuguang

last: Zhang


title: Arabidopsis buds: ahl16 vs. Col-0

status: Public on Apr 04 2014

city: Shanghai

first: Zhong-Nan

address: Shanghai Guilin Road No.100

institute: Shanghai Normal University

summary: Transcriptional profiling of Arabidopsis buds comparing ahl16 mutants with wild type (Col-0 ecotype). Goal was to determine the differential expression genes between the buds of mutant and wild type.

overall_design: Biological replicates: 3 replicates of mutant buds, 3 replicates of wildtype buds.

first: Zhong

first: Jun

last: Zhu


title: An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks [Affymetrix]

status: Public on Jun 17 2014

city: Madison

first: Timothy

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

summary: Rhodobacter sphaeroides is the best studied photosynthetic bacterium, yet much remains unknown about its transcriptional regulatory processes on a genome-scale. We developed a work-flow for genome-scale reconstruction of transcriptional regulatory networks and applied it to sequence and gene expression data sets available for R. sphaeroides. To assess the predictive performance of our reconstructed model, we generated global transcript level and/or protein-DNA interaction data for 3 transcription factors (PpsR, RSP_0489 and RSP_3341). This dataset contains global transcript level analyses for RSP_0489 and RSP_3341 deletion strains, as well as matching wild type controls.

overall_design: Microarray analysis conducted for deletion strains of 2 previously uncharacterized transcription factors predicted to be involved in the regulation of carbon metabolism and iron homeostasis in R. sphaeroides using the R. sphaeroides Affymetrix gene chip. These deletion mutant expression profiles were compared to that of wild type cells to determine differentially expressed genes regulated by these transcription factors.

first: Saheed

last: Imam


title: DNA methylation data from hepatoma

status: Public on Jul 15 2014

city: Kawasaki

first: Yoshiyuki

last: Watanabe

state: Kanagawa

address: 2-16-1 Sugao Miyamaeku

department: Department of Internal Medicine, Division of Gastroenterology and Hepatology

institute: St.Marianna University School of Medicine

summary:
To identify methylation levels of primary hepatoma (HCC) and cells
We used microarray to detail the global programme of DNA methylation in HCC

overall_design: HCC vs. Human blood DNA.

first: Hiroyuki

last: Yamamoto


title: microRNA expression in skin and wound edge tissue at different time points

status: Public on Mar 06 2014

city: Columbus

first: Chandan

last: Sen

state: Ohio

address: 473W. 12th Avenue,

department: Surgery

institute: Ohio State University Wexner Medical Center

summary: Change in miRNA expression pattern during different phases of wound healing following full thickness excisional wounding was studied.

overall_design: In the study presented here, a comprehensive profiling of all the mouse/rat miRs annotated in the miRBase 8.0 was performed using the FlexmiR™ MicroRNA Labeling Kit

first: Jaideep

last: Banerjee

first: Subhadip

last: Ghatak


title: PSY1 responding transcripts in two plant lines of Arabidopsis thaliana

status: Public on Mar 08 2014

city: Slagelse

first: Khalid

last: Mahmood

address: Forsøgsvej 1

department: Agro-ecology

country: Denmark

institute: Aarhus University

summary: Plant peptide containing sulfated tyrosine 1 (PSY1) has been reported to promote cell expansion and differentiation in the elongation zone of roots. To further understanding of PSY1 based cell elongation, a full genome microarray study was conducted on wild type and receptor (psy1r) mutant plants after PSY1 treatment. This approach led us to elucidate the components involved in PSY1 based cell elongation.

overall_design: Two plant lines (Wild type and psy1r) were grown hydroponically for one week and following treated with 10 nM PSY1 for 4 hr before RNA extraction for micorarray. Three independent biological samples were prepared

first: Anja

last: Fuglsang

first: Kirsten

last: Jørgensen


title: ThERF1 regulates its target genes via binding a novel cis-acting element in response to salt stress

status: Public on May 21 2014

first: Liuqiang

last: Wang

address: 26 Hexing Road

institute: Northeast Forestry University

summary: To reveal the regulatory network of ThERF1 in response to abiotic stress, we have employed an Agilent Arabidopsis gene expression microarray to study the expression profile changes between Wild-type and transgenic plants overexpressing ThERF1 under salt stress. A total of 154 and 307 differentially expressed genes with p-value < 0.05 and ≥ 2-fold change were significantly up- and down- regulated in ThERF1-transformed plants under salt stress treatment.

overall_design: Four-week-old seedlings of Wild-type and ThERF1-transformed Arabidopsis plants treated with 120 mM NaCl for 6 h were immediately harvested for RNA isolation. The Agilent Arabidopsis (V4) gene expression microarray (4× 44K, Design ID: 021169) was employed to compare the gene expression profiles of Wild-type and transgenic plants with three independent biological replicates.

first: Yucheng


title: Construction of gene expression profiles for anoxia-reoxygenation in Arabidopsis

status: Public on Feb 18 2014

city: Taipei

first: Kuen-Jin

last: Tsai

address: 128 Academia Road, Section 2, Nankang

department: Agricultural Biotechnology Research Center

institute: Academia Sinica, Taiwan

summary: To understand how plants respond to anoxia-reoxygenation, we have employed a global microarray expression profiling as a basic platform to characterize genes with the potential to mediate the recovery responses in Arabidopsis. 7-day-old seedlings were trated with 4hr and 8hr anoxia, and then reoxygenated in air for 0, 0.5, 1, 3, 6 hrs. Genes changed in both condition were designated as reoxygenation-regulated genes. They included the genes in ROS detoxification, dehydration, metabolic process, and many other responses. Interestingly, ethylene was also involved in this recovery process. We further adopted ein2-5 and ein3eil1 microarray to investigate ethylene signaling. Our results showed ethylene partially regulate reoxygenation regulated genes and is reruired for plant survival in reoxygenation.

overall_design: Genes expression during anoxia-reoxygenation in Arabidopsis seedlings was measured at 0, 0.5, 1, 3, 6 hours after anoxia treatment, and normal condition before anoxia. Three independent experiments were performed at each time (Nor, 0, 0.5, 1, 3, 6) under 4hr anoxia-reoxygenation condition by using Col-0, ein2-5, and ein3eil1. Four independent experiments were performed at each time (Nor, 0, 0.5, 1, 3, 6) under 8hr anoxia-reoxygenation condition by using Col-0.


title: Combined stress treatment of high salinity, osmotic pressure and heat to Arabidopsis thaliana

status: Public on Mar 05 2014

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: In natural habitats, plants are often exposed to multiple stresses. Most studies, however, for plant abiotic stress responses analyzed those to individual stress but not combined stresses. In this report, we performed comparison analyses of gene expression to individual stresses, salt, osmotic and heat, and to a combination of these three stresses, which mimics arid conditions. We show here that the combined stress treatment induces unique gene expression pattern but not a simple reflection of the additive effects of individual stresses. First, the number of genes induced by combined stresses (150 mM NaCl, 200 mM mannitol and 35°C heat) was much smaller when compared to the sum of those induced by individual stress treatments, while the number of genes downregulated by multiple stresses was larger.  A large number of genes induced by mannitol were not induced by multiple stresses, while those induced by salts were less affected in combined stress treatments. In addition, 125 genes, including13 for transcription factors, were found to be induced specifically by combined stress treatments. We report here that the plant response to a multi-stress environment represents an output of complex interactions between different stress aspects and signaling events of the various components of this environmental situation, and the determinative factor in this response is to avoid/minimize the antagonistic effects and to magnify the synergistic features of the imposed environmental challenges. Based on our results, we propose that genes that are highly induced by multiple treatments may be candidate for engineering stress tolerant crop plants.

overall_design: Wild-type plants of Arabidopsis thaliana were treated with three abiotic stresses, high salinity (150mM and 300mM), high osmotic pressure (200mM and 400mM mannitol) and heat (35°C), individually or simultaneously. Plants were treated with salt or mannitol for 16 hrs (first 1 hr and last 7 hrs are in light and other time in dark) or with heat for 4 hrs (in light) before sampling. There are three biologcal replicates.

first: Sewelam

last: Nasser

first: Mitsuda

last: Nobutaka

first: Ohme-Takagi

last: Masaru


title: Identification of genes cooperatively regulated by cytokinin and HD-ZIP III transcription factors

status: Public on Jan 29 2014

first: Tian-Qi

last: Zhang

address: 300 Fenglin Road

department: Plant Molecular Genetics

institute: Institute of Plant Physiology and Ecology

summary: In Arabidopsis thaliana, cytokinin responsive B-type ARR transcription factors and HD-ZIP III transcription factors such as REVOLUTA (REV), act cooperatively as master regulators of shoot regeneration. To identify the downstream targets of ARR-HD-ZIP III transcriptional complex, we used an inducible line of REV, 35S::FLAG-GR-rREV, in which FLAG-tagged miR165/6-non-targetable form of REV (rREV)-GR fusion protein was expressed from 35S promoter. DEX treatment induced activation of REV by translocation of FLAG-GR-rREV fusion protein from cytoplasm to the nucleus. We treated 35S::FLAG-GR-rREV seedlings with  6-benzylaminopurine (6-BA, a cytokinin), dexamethasone (DEX), or 6-BA+DEX for 2 hours. Total RNAs were extracted and subjected to Agilent Arabidopsis Gene Expression Microarray analyses. The differentially expressed genes (>1.5-fold, p<0.05) were identified.

overall_design: 10-day-old 35S::FLAG-GR-rREV plants were treated with 6-benzylaminopurine (6-BA), dexamethasone (DEX), or 6-BA+DEX for 2 hours. DEX treatment induced activation of REV by translocation of FLAG-GR-rREV fusion protein from cytoplasm to the nucleus. Total RNA was extracted with RNeasy Mini Kit and hybridized to Agilent Arabidopsis Gene Expression Microarray. Differentially expressed genes were defined by a 1.5-fold expression difference with a P value<0.05. Biological replicates were performed.

first: Jia-Wei


title: Arabidopsis hsi2 vs. Col-0 Drought Arrays

status: Public on Jan 24 2014

city: Saskatoon

first: Pierre

last: Fobert

address: 110 Gymnasium Place

institute: National Research Council Canada

summary: Transcriptional profiling of rossette leaves comparing wild type (Col-0) and the mutant (hsi2-5) under no drought or simulated drought stress.

overall_design: Two-condition experiment; wild type (col-0) vs. mutant (hsi2-5). Three stages of drought; no drought (or stage 0), mild drought or soil drying but no visible wiliting (or stage 1), visible wilting (stage 2). At stage 0, four biological replicates of the wild type/mutant co-hybridized, at stage 1 and stage 2, three biological replicates of the wild type/mutant co-hybridized.

first: Nirmala

last: Sharma

first: Yarnel

last: Bender

first: Kerry

last: Boyle


title: Mapping of somatic linker histone H1 variants in T47D-MTVL and HeLa cells

status: Public on Feb 04 2014

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

institute: IBMB-CSIC

summary: At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the different variants have specific roles, are distributed differentially along the genome, or regulate specific promoters. By taking advantage of specific antibodies to H1 variants and HA-tagged recombinant H1 variants expressed in a breast cancer-derived cell line, we have investigated the distribution of the different somatic H1 variants (H1.2 to H1.5, H1.0 and H1X) in particular promoters and genome-wide.

overall_design: Analysis of H1 (H1.0, H1.2, H1.3, H1.4, H1.5 and H1X) and H3 abundance in promoter regions

first: Lluís

last: Millán-Ariño


title: VuDREB2A activated transcription in wild type Arabidopsis: VuDREB2A overexpressor lines vs. wild type Arabidopsis

status: Public on Dec 10 2013

city: Guwahati

first: Ayan

last: Sadhukhan

state: Assam

address: IIT GUwahati, Amingaon, North Guwahati

department: Biotechnology

institute: Indian Institute of Technology Guwahati

summary: Transcriptional profiling of Arabidopsis overexpressing VuDREB2A (full length/truncated) compared to wild type. Unstressed three week-old whole seedlings were used. Goal was to search the genes upregulated byVuDREB2A in Arabidopsis.

overall_design: Two-condition experiment, VuDREB2A (full length/truncated) overexpressing lines v.s. wild type. Biological replicates: 2 transgenic replicates, 2 wild type replicates

first: Yasufumi

last: Kobayashi

first: Hiroyuki

last: Koyama


title: Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations

status: Public on Nov 21 2013

city: Paterna

first: Jordi

last: Tronchoni

address: Avda. Agustín Escardino, 7

institute: CSIC

summary: Comparative genome-wide gene expression analysis between a wine yeast strain belonging to the species S. cerevisiae and the type strain from S. kudriavzevii IFO1802, a cryotolerant yeast, in natural must fermentations.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces kudriavzevii

overall_design: RNA samples taken from wine fermentations at 12ºC and 28ºC at the beginning of exponential phase. Three biological replicates.

first: Victor

last: Medina

first: Jose

last: Guillamón

first: Amparo

last: Querol

first: Roberto

last: Pérez-Torrado


title: Genome-wide Analysis of Enterococcus faecalis OG1RF Gene Expression During Infection

status: Public on Dec 15 2013

city: Minneapolis

first: Kristi

middle: L

last: Frank

state: MN

address: 420 Delaware St SE, MMC196

department: Dept. of Microbiology

institute: University of Minnesota

summary: Changes in Enterococcus faecalis OG1RF gene expression during infection in a rabbit model of subdermal abscess formation were studied using microarray analysis.

overall_design: Samples assayed in arrays consisted of the input inoculum and total RNA collected from the subdermal chambers at 2 and 8 hours post-inoculation.  Alexa647-labeled samples were co-hybridized with 0.5 micrograms of sheared OG1RF genomic DNA labeled with Cy3 as a standard reference between chips.  Four biological replicates were performed for each of the 3 time points.

first: Suzanne

last: Grindle

first: Gary

last: Dunny