title: Expression profiling of myeloid leukemia cell treated with vibsanin A, PMA and ATRA

status: Public on Feb 28 2016

city: Beijing

first: Yu

last: Zuyin

address: No. 27 Taiping Road

department: Department of Pathophysiology

institute: Beijing Institute of Radiation Medicine

summary:
All-trans retinoic acid (ATRA)-based differentiation therapy has achieved success with the treatment of acute promyelocytic leukemia (APL), a unique subtype of acute myeloid leukemia (AML). However, other subtypes of AML display resistance to ATRA-based treatment. Here, we demonstrate that a novel natural vibsane-type diterpenoid vibsanin A promotes the differentiation of myeloid leukemia cell lines and primary AML blasts.
To reveal how vibsanin A function on promoting myeloid leukemia cell differentiation, we analyzed and compared the gene expression profiles in myeloid leukemia HL-60 cells treated with vibsanin A, PMA, and ATRA.

overall_design: HL-60 cells were treated with vibsanin A, PMA and ATRA for 6 hours or longer up to 24 hours. Gene expression profiling was conducted

first: Cong

last: Yuwen


title: Neuronal and glial Gene expression from control and healthy patient iPSC-derived forebrain neurons (A)

status: Public on Jan 06 2016

city: Boston

first: Tracy

last: Young-Pearse

state: MA

address: HIM 760, 77 Avenue Louis Pasteur

department: Ann Romney Center For Neurologic Disease

country: USA

institute: Brigham and Women"s Hospital

summary: Neuronal or glial cell fates related gene expression from single cells with variety of sAPPa or total Aβ secretion profiles were presented here.

overall_design: Single living human iPSC-derived forebrain neuronal cells with variety of sAPPa or total Aβ secretion profiles were selected and examined for gene expression.

first: Meichen

last: Liao


title: Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways

status: Public on Feb 16 2016

city: Utrecht

first: Basten

last: Snoek

address: Padualaan

department: Mol. Plant. Physiology

country: Netherlands

institute: Utrecht University

summary: Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains Bristol N2 and Hawaii CB4856 to enable quantitative trait loci (QTL) mapping. Variation in gene expression was greater in the RILs than in the parental lines, at the proteome as well as at the transcriptome levels. We detected a trans-QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels.

overall_design: Parental genotypes N2 (3x) and CB4856 (3x) and 47 RILs from (Li etal 2006; Vinuela etal 2010 and Elvin etal 2011)

first: Kapil Dev

last: Singh

first: Bernd

last: Roschitzki

middle: L

first: Jonas

last: Grossmann

first: Xue

last: Zheng

first: Mark

last: Elvin

first: Polina

last: Kamkina

first: Sabine

middle: P

last: Schrimpf

first: Gino

middle: B

last: Poulin

first: Jan

middle: E

last: Kammenga

first: Michael

middle: O

last: Hengartner


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

status: Public on Mar 07 2016

city: Budapest

first: Krisztian

last: Papp

address: 1/C Pazmany P.

country: Hungary

institute: MTA-ELTE Immunology Research Group

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

platform_organism:
Homo sapiens
Bos taurus
Capra hircus

overall_design: Refer to individual Series


title: Genomic Run On (GRO): determination of the nascent transcriptional rates in a series of Hrp1 mutants.

status: Public on Dec 31 2015

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary: The goal of the project was to check the differential effect on transcription rate of a sudden degron-induced depletion of Hpr1 protein and its comparison towards the effect of a constitutive absence of Hpr1 protein in a deletion strain.

overall_design: Cells were grown in YP-Raffinose + 0.1 mM CuSO4  at 26ºC to 0.5 OD600. At that cells were spun-down and changed to YP-Galactose without CuSO4 for 30 min at 26ºC. Then cells were shifted to 37ºC to induce degron-mediated proteolysis and recovered after 30 min. Samples include wt, hpr1delta and hpr1-degron after 0 or 30 min growth at 30ºC.

first: José

last: Pérez-Ortín

first: Antonio

last: Jordán-Pla

last: García-Martínez


title: Gene expression of F.graminearum during maize stalk infection

status: Public on Feb 11 2016

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

country: China

institute: Shanghai Inst. Plant Phys. & Eco.

summary:
Fusarium graminearum can infect maize stalk causing Gibberella stalk rot.
We want to know the whole genome wide gene profiling when infecting maize stalk.

overall_design: Using lasr capture microdisecction, we captured 8 time points infecting hyphae samples for maize stalk and after two-round amplification, we hybrid the aRNA to Affymetrix array.

first: Yan

last: Zhang


title: Transcriptomic analysis using olive varieties and breeding progenies identify candidate genes involved in plant architecture.

status: Public on Feb 15 2016

city: Zagreb

first: Juan Jose

last: Gonzalez Plaza

address: Mirogojska 8

department: Research Department

country: Croatia

institute: University Hospital for Infectious Diseases "Dr. Fran Mihaljevic"

summary:
Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Most of the existing varieties of olive are traditional and their architecture is poorly suited for modern growing and harvesting systems. This study focuses on the identification of candidate genes involved in determining plant architecture in olive that could help in selecting phenotypes adapted to modern cultivation practices.
We previously developed the first microarray for olive, as a means to discover candidate genes involved in relevant agronomical traits. The microarray has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. In the present study, made in the framework of an olive breeding program, varieties displaying differences in architecture and pooled seedlings grouped by their architecture-related phenotypes, were analysed using microarray analysis of meristematic tissue.
We identify 2,258 differentially expressed genes potentially involved in determining plant architecture. Varieties with opposite architecture phenotypes and individuals from segregating progenies displaying extreme architecture features, constitute our key to linking phenotype to expression. We analyze some of the genes with potentially interesting functional annotation using quantitative RT-PCR assays, in the reference varieties and individual seedlings. Arabidopsis mutants in putative orthologs of some of the candidate genes show altered architecture, indicating functional conservation between the two species and supporting both, the biological relevance of the results, and the potential of the identified genes as markers for assisted breeding for olive varieties suited for high density orchards.

overall_design: Active or dormant meristems to be used for expression analysis were collected from individual olive trees from four varieties Picual, Arbequina, Arbosana and Chiquitita and from seedlings of a Picual x Arbequina progeny, all of the showing variability for growth habit. Plant material was provided by the olive breeding program of Cordoba. Harvesting was carried out between 8:00 to 11:00 a.m., at the end of Spring. Samples were immediately frozen in liquid nitrogen, and maintained afterwards at -80 ºC. Samples of the Picual x Arbequina seedlings used to generate pools were harvested individually and 0.2 g of tissue per individual mixed and processed together to obtain RNA to be used for microarray analysis.

first: Juan

middle: J

first: Carmen

last: Beuzon


title: Comparative analysis of genome-wide gene expression profiles in heart, liver, spleen, ears and bone marrow in the murine strains of MRL/MpJ, C57B/6J, and Balb/C

status: Public on Dec 30 2015

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

department: Molecular Biotechnology and Microbiology

country: Poland

institute: Gdansk University of Technology

summary: The MRL/MpJ mouse strain is known as a model of mammalian regeneration. The strain exhibits an unusual capacity in regenerative wound healing manifested by scarless ear-hole closure and enhanced regeneration response reported in other organs. A significant feature of the strain is that the adult MRL/MpJ mouse retains several embryonic biochemical characteristics, including increased expression of stem cell markers. As the regenerative response after injury is rather limited in mammals the MRL/MpJ mouse is a great model to study the molecular and cellular basis of scarless wound healing. We report here the analysis of genome-wide transcriptomic profiles in the heart, ear, spleen, liver and bone marrow of the MRL/MpJ mouse. We used gene expression microarray, which interrogates 44.170 of mouse transcripts, in order to identify the genes exhibiting remarkable differences in expression in the MRL/MpJ mouse compared to two reference strains: C57BL/6J and BALB/c. The comparison revealed hundreds of differentially expressed transcripts. Significant enrichments of genes engaged in retinol metabolism, peroxisome proliferator-activated receptor (PPAR), wound healing, and homeobox pathways distinguishes the differentially expressed transcripts up-regulated in the MRL/MpJ mouse, whereas the genes related to immune response, including including response to wounding are greatly enriched among those down-regulated. The same functional categories were associated with remarkable parallels between the transcriptomic patterns in murine neonates and the adult MRL/MpJ mouse.

overall_design: 15 samples, each sample is a poll representing three animals

first: Paweł


title: DNA Methylation in Paraganglioma

status: Public on Dec 25 2015

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

institute: Spanish National Cancer Research Centre (CNIO)

summary: We performed a whole-genome DNA methylation assay (27K Illumina) in a large, well characterized Discovery Series of 123 PPGL with (n=24) and without (n=99) metastases.

overall_design: Bisulphite converted DNA from the 123 PPGL samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Aguirre

middle: A

last: de Cubas


title: Transcriptome analysis of male flowers corresponding to anther developmental stages in Cryptomeria japonica

status: Public on Mar 01 2016

city: Hitachi

first: Miyoko

last: Tsubomura

state: Ibaraki

department: Forest Tree Breeding Center

country: Japan

institute: Forestry and Forest Products Research Institute

summary: Investigation of gene expression changes among anther development in wild type and male sterile mutant.

overall_design: Male strobili of wild-type were collected at 10 stages with three biological repeats (total 30 samples) and male strobili of mutant were collected at stages 3 to 6 with three biological repeats (total 12 samples).

first: M

last: Kurita

first: A

last: Watanabe


title: Adjunctive therapy with a phosphodiesterase-4 inhibitor improves INH response to pulmonary tuberculosis

status: Public on Dec 21 2015

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: PHRI, NJMS, Rutgers the State University of NJ

summary:
Current antibiotic regimen to treat tuberculosis (TB) is ineffective in fully eliminating the bacterial load and in alleviating disease pathology. We examined the usefulness of a phosphodiesterase-4 inhibitor (CC-11050) as an adjunctive to anti-TB drug Isoniazid (INH) to improve the outcome of treatment in a rabbit model of active pulmonary TB.  Control of Mycobacterium tuberculosis (Mtb) growth, disease pathology and the global transcriptional response in Mtb-infected lungs of rabbits with or without CC-11050 treatment were studied.
The microarray experiments involves comparison of changes in gene expression between uninfected and Mtb-HN878 infected (Untreated) or CC-11050  treated rabbit lungs at 8 weeks post-treatment, starting at 4 weeks of infection (i.e, 12 weeks post infection).

overall_design: New Zealand White rabbits were infected with Mtb HN878 at about 3.2log10 (on day 0).  Starting at 4 weeks post infection, group of rabbits (n=4 per group) were treated with CC-11050 or no treatment. A group of uninfected rabbits were used as controls.  Total RNA from lung tissues of uninfected and Mtb-infected with or without treatment were isolated at 8 weeks post treatment and used for microarray gene expression analysis using 4X44k Agilent Rabbit Microarray system

first: Gilla

last: Kaplan


title: Different gene expression signatures in children and adults with celiac disease

status: Public on Dec 19 2015

first: Concepción

last: Núñez

address: C/Profesor Martín Lagos

department: Inmunología Clínica

institute: Instituto de Investigación Sanitaria Hospital Clínico San Carlos

summary: We collected 19 duodenal biopsies of children and adults with celiac disease and compared the expression of 38 selected genes between each other and with the observed in 13 non-celiac disease controls matched by age.

overall_design: qPCR gene expression profiling. Intestinal samples from children and adults with active celiac disease patients and controls were analysed.

first: Virgina

last: Pascual

first: Luz

middle: M

last: Medrano

first: Natalia

last: López-Palacios

first: Andrés

last: Bodas

first: Bárbara

last: Dema

first: Miguel

last: Fernández-Arquero

first: Beatriz

last: González-Pérez

first: Isabel

last: Salazar


title: The Arabidopsis type-B cytokinin response regulators ARR1, ARR10 and ARR12 negatively regulate plant responses to drought

status: Public on Jan 13 2016

city: Hanoi

first: Kien

middle: Huu

last: Nguyen

state: Bac Tuliem

address: Pham Van Dong str., Bac Tuliem, Hanoi, Vietnam

department: Genetic Engineering Department

country: Viet Nam

institute: Agricultural Genetics Institute

summary: To understand the role of the Arabidopsis type-B Response Regulators ARR1, ARR10 and ARR12 in water stress response, we have carried out comparative expression analysis of the arr1,10,12 mutant and WT plants under dehydration and well-watered (control) conditions. Agilent’s whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Two-week-old WT and arr1,10,12 mutant plants were transferred from GM plates to soil and grown for 10 additional day. Aerial portions of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 4 h. Rosette leaves collected in 3 biological repeats from arr1,10,12 and WT plants treated by dehydration for 0, 2 and 4 h were used for microarray and expression analyses. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.

middle: H

first: Chien

middle: V

last: Ha

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Lam-Son

last: Tran


title: The Six1 oncoprotein represses translation of p53 via concomitant regulation of RPL26 and microRNA-27a

status: Public on Jan 15 2016

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary: TP53 is mutated in 50% of all cancers, and is often functionally compromised in cancers where it is not mutated.  We demonstrate that the pro-tumorigenic/metastatic Six1 homeoprotein decreases p53 levels through a mechanism that does not involve the negative regulator of p53, MDM2. Instead, Six1 regulates p53 via a dual mechanism involving upregulation of microRNA-27a and downregulation of the ribosomal protein L26 (RPL26), a positive regulator of p53 translation. Mutation analysis confirms that RPL26, whose expression inversely correlates with Six1 expression in numerous tumor types, inhibits miR-27a binding to the p53 3’UTR and prevents microRNA-mediated translational inhibition of p53. Thus, through simultaneous downregulation of RPL26 and upregulation of miR-27a, Six1 efficiently lowers p53 levels despite regulation of p53 at the level of the proteasome.  Consequently, Six1 overexpression, which is observed in numerous tumor types, leads to dramatic resistance to nutlins, as well as other therapies targeting the p53-MDM2 interaction.

overall_design:
Two samples were profiled in triplicates.  66cl4 scrambled and 66cl4 with shRNA knockdown of SIX1.
Knockdown experiment

first: Aik-Choon

first: Christina

last: Garlington

first: Heide

last: Ford


title: Neuronal and glial Gene expression from control and healthy patient iPSC-derived cortical neurons

first: Tracy

last: Young-Pearse

sample_organism:
Homo sapiens
unidentified


title: Genomic Run On (GRO): determination of the nascent transcriptional rates in a series of a mex67 mutant.

first: Jose

last: Perez-Ortin

summary: The goal of the project was to check the effect on transcription rate of a sudden depletion of Mex67 protein by using a thermosensitive mutant: mex67-5

overall_design: Cells were grown in YPD at 26ºC to 0.5 OD600. At that time cells were shifted to 37ºC to induce Mex67 protein inactivation and recovered after, 0, 5, 20, 40, 60 and 150 min.

first: José

last: Pérez-Ortín

first: Antonio

last: Jordán-Pla

last: García-Martínez


title: Single cell analysis defines the divergence between the innate lymphoid cell and lymphoid tissue inducer lineages

city: New York

first: Herman

last: Gudjonson

state: NY

address: 417 E 68th St

department: Computational and Systems Biology Program, SKI

institute: Memorial Sloan Kettering Cancer Center

summary: The precise lineage relationships between innate lymphoid cells (ILC) and the lymphoid tissue inducer (LTi) are poorly understood. Using single-cell multiplex transcriptional analysis of 100 lymphoid genes and single-cell cultures of fetal liver precursor cells, we identified the common proximal precursor to these lineages and showed that its bifurcation was precisely marked by the differential induction of the transcription factors PLZF and TCF1. Acquisition of individual ILC1/2/3-specific effector programs was initiated later, at the common ILC precursor (ILCP) stage, by transient expression of mixed ILC1/2/3 transcriptional patterns whereas, in contrast, LTi development did not go through multilineage priming. These findings provide novel insights into divergent mechanisms of ILC and LTi lineage differentiation and establish a high-resolution map of their development.

overall_design: We performed transcriptional analysis of single cells along the fetal pathway spanning the differentiation of the common lymphoid precursor into innate lymphoid cells (ILCs) and lymphoid tissue inducer (LTi) with the Biomark Fluidigm multiplex qRT-PCR system, using a panel of 100 lymphoid development factors including transcription factors, cytokine receptors and chemokine receptors. Data from 339 single precursor cells (Lin- IL7Rα+α4β7+), including 157 αLPs (PLZF-CXCR5-), 168 ILCPs (PLZF+), and 14 LTiPs (PLZF-CXCR5+) were compiled from two independent single-cell sorting experiments using pooled E15 fetal livers. After filtering by housekeeping gene expression, we considered the transcriptional profiles from 299 single cells for downstream analysis.

last: Ishizuka

first: Sylvestre

last: Chea

first: Michael

middle: G

last: Constantinides

first: Aaron

middle: R

last: Dinner

first: Albert

last: Bendelac

first: Rachel

last: Golub


title: High-resolution mapping of homologous recombination events in rad3 hyper-recombination mutants

city: Durham

first: Thomas

middle: D

last: Petes

state: NC

address: 213 Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

type: Genome variation profiling by genome tiling array

summary: The Saccharomyces cerevisae RAD3 gene is homolog of human XPD, an essential gene encoding a DNA helicase of the TFIIH complex involved in both nucleotide excision repair (NER) and transcription. Mutant alleles of RAD3 have been identified (rad3-101 and rad3-102) that have partial defects in DNA repair associated with a strong hyper-recombination (hyper-Rec) phenotype. Previous studies showed that the hyper-Rec phenotype associated with rad3-101 and rad3-102 can be explained as a consequence of persistent single-stranded DNA gaps that are converted to recombinogenic double-strand breaks (DSBs) by replication. We have further characterized these events using a system in which the reciprocal products of mitotic recombination between homologs are recovered as red and white sectored colonies. Both rad3-101 and rad3-102 elevate the frequency of sectored colonies about 100-fold. Subsequent mapping of these events shows that three-quarters of crossovers between homologs induced in hyper-Rec rad3 mutants reflect DSBs formed in at the same positions in both sister chromatids (double sister-chromatid breaks, DSCBs). The remainder reflects DSBs formed in single chromatids (single chromatid breaks, SCBs). The ratio of DSCBs to SCBs is similar to that observed for spontaneous recombination events in wild-type cells. In addition to examining crossovers on chromosome V, we mapped 216 unselected genomic alterations throughout the genome including crossovers, gene conversions, deletions, and duplications. We found a significant association between the location of these recombination events and regions with elevated gamma-H2AX. In addition, there was a hotspot for deletions and duplications at the IMA2 and HXT11 genes near the left end of chromosome XV. A comparison of these data with our previous analysis of spontaneous mitotic recombination events suggests that a sub-set of spontaneous events in wild-type cells may be initiated by incomplete NER reactions, and that DSCBs, which cannot be repaired by sister-chromatid recombination, are a major source of mitotic recombination between homologous chromosomes.

overall_design: This experiment involves the analysis of 96 two-color microarrays. 86 of the microarrays represent the analysis of 43 red/white sectored colonies in which the sectors have the reciprocal products of a mitotic recombination event on chromosome V. In 68 of these 86 microarrays, we used SNP arrays in which recombination events throughout the genome could be analyzed (whole-genome arrays; abbreviated WG in the files below). The strains used in this analysis (MD555 and MD556) were independent isogenic strains that were homozygous for the rad3-102 mutation; 40 arrays were examined for MD555 and 26 arrays were examined for MD556. We also examined ten sectored colonies derived from the strain SLA64 (20 of 86 microarrays). This strain is identical to MD555 and MD556 except that it is homozygous for the rad3-101 allele instead of the rad3-102 allele .For two of these sectored colonies (four arrays), we used the whole genome microarrays.  For the other eight sectored colonies (16 microarrays), we used microarrays that had dense arrays of oligonucleotides specific for chromosomes I, III, V, and the right arm of chromosome VIII; in addition, the arrays had oligonucleotides representing the telomeres and centromeres of the other yeast chromosomes. Below, we use the designation VA (chromosome V-specific arrays) in the file names. Finally, we examined ten whole-genome arrays in which sub-cultured strains were analyzed; five were derived from MD555, and five from SLA64. For all experiments, genomic DNA from the experimental strain was labeled with Cy5-dUTP and from the control isogenic wild-type diploids (PG311 or JSC23, as indicated below) with Cy3-dUTP. The strains PG311 and JSC23 are described in detail in Lee et al. (2009) PLoS Genetics 5: e1000410 and Yin and Petes (2013) PLoS Genetics 9: 1003894, respectively.

first: Sabrina

last: Andersen

first: Aimee

last: Zhang

first: Margaret

last: Dominska

first: Maria

last: Moriel-Carretero

first: Emilia

last: Herrera-Moyano

first: Andres

last: Aguilera


title: Transcript level coordination of carbon pathways during silicon starvation induced lipid accumulation in the diatom Thalassiosira pseudonana

city: La Jolla

first: Sarah

middle: R.

last: Smith

state: CA

address: 9500 Gilman Dr.

department: Scripps Institution of Oceanography

institute: University of California, San Diego

summary: Nutrient-starvation induced lipid accumulation has been reported in diverse algae, including diatoms. Molecular mechanisms underlying lipid accumulation in nutrient-starved algae are of interest to inform genetic engineering strategies aimed at improving lipid productivity. Diatom cell walls are made of nanostructured silica which is a unique feature of the group and silicon deprivation induces both growth arrest and lipid accumulation. In this work, we report the whole cell transcript level response during silicon starvation induced lipid accumulation.

overall_design: Analyzed mRNA from cells after 0, 4, 8, 12, 18, and 24 hr of silicon starvation using the Affymetrix GeneChip whole genome tiling array. Initial analysis of gene level expression was performed using the Affymetrix Expression Console Software, version 1.1. No biological replicates were performed. 0 hr is used as a reference point.

first: Corine

last: Glé

first: Raffaella

last: Abbriano

first: Jesse

middle: C

last: Traller

first: Aubrey

middle: K

last: Davis

first: Emily

last: Trentacoste

last: Vernet

first: Andrew

last: Allen

first: Mark

last: Hildebrand


title: Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase (ChIP)

status: Public on Dec 18 2015

city: Los Angeles

first: Jared

last: Peace

state: CA - California

address: 1050 Childs Way RRI 203

department: Molecular and Computational Biology

institute: University of Southern California

type: Genome binding/occupancy profiling by array

summary: The S. cerevisiae Forkhead Box (FOX) proteins, Fkh1 and Fkh2, regulate diverse cellular processes including transcription, long-range DNA interactions during homologous recombination, and replication origin timing and long-range origin clustering.  As stimulators of early origin activation, we hypothesized that Fkh1 and Fkh2 abundance limits the rate of origin activation genome-wide.  Existing methods, however, were not well suited to quantitative, genome-wide measurements of origin firing between strains and conditions.  To overcome this limitation, we developed qBrdU-seq, a quantitative method for BrdU incorporation analysis of replication dynamics, and applied it to show that overexpression of Fkh1 and Fkh2 advance the initiation timing of many origins throughout the genome resulting in a higher total level of origin initiations in early S phase.  The higher initiation rate is accompanied by slower replication fork progression, thereby maintaining a normal length of S phase without causing detectable Rad53 checkpoint kinase activation.  The advancement of origin firing time, including that of origins in heterochromatic domains, was established in late G1 phase, indicating that origin timing can be reset subsequently to origin licensing.  These results provide novel insights into the mechanisms of origin timing regulation by identifying Fkh1 and Fkh2 as rate-limiting factors for origin firing that determine the ability of replication origins to accrue limiting factors and have the potential to reprogram replication timing late in G1 phase.

overall_design: 6 samples, 3 replicates of 2 strains

first: Sandra

last: Villwock

first: John

middle: L

last: Zeytounian

first: Yan

last: Gan

first: Oscar

last: Aparicio


title: G72 overexpression in U87 cells

city: Taichung Ciy

first: Hao-Teng

last: Chang

address: No.91, Hsueh-shih Rd. N. Dist.

country: Taiwan

institute: China Medical University

summary: G72 is a susceptible gene for schizophrenia. No matter genetic variation or serum levels, G72 has been recognized as a biomarker for schizophrenia. In some reports, G72 genetic variation also related with bipolar disorder. Although G72 has been studied for 15 years, the protein function is still unclear. This study aims for predicting the biological function of G72 and hope to elucidate its biological role.

overall_design: two independent control (U87 cells transfected with empty vector) and two experiements (U87 cells transfected with G72 overexpression plasmid).


title: Expression data from third instar Drosophila larvae

city: hyderabad

first: amitava

last: basu

state: andhra

address: jn road

country: India

institute: cdfd

summary:
Ectopic expression of DNMT3L in Drosophila causes melanotic tumor in the transgenic flies from fifth generation onwards.
We used microaarray data analysis to look for the genes and pathways which are affected on ectopic expression of DNMT3L in Drosophila.

overall_design: Drosophila third instar larvae were selected at particular stages of development for RNA extraction and hybridization on Affymetrix microarrays.

first: Amitava

last: Basu

first: Archana

last: Tomar

first: Sanjeev

last: Khosla


title: Transcription profiling by array of yeast single and double deletion mutants of gene-specific transcription factors

status: Public on Dec 24 2015

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

institute: UMC Utrecht

summary: Contains gene expression profiles of yeast single and double deletion mutants of gene-specific transcription factors. Genetic interactions were studied by comparing gene expression changes of double mutants with gene expression changes in the respective single mutants. Pairs of gene-specific transcription factors were chosen based on previous evidence for epistasis, including synthetic genetic interactions as well as common DNA binding.

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Using the Erlenmeyer growth protocol up to five deletion strains were grown on a single day. In the tecan platereader, up to eleven deletion strains could be grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.

first: Katrin

last: Sameith

first: Frank

last: Holstege


title: Gene expression profiles in lymph nodes with metastasis of oral squamous cell carcinoma (OSCC)

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

summary:
Background: Cervical lymph node metastasis is a potent prognostic factor in oral squamous cell carcinoma (OSCC). However, lymph nodes resected by sentinel node biopsy or neck dissection are usually diagnosed by examining only one or two sections of the maximal cut surface. Accurate diagnosis of the metastasis in lymph nodes is important but depends on a heavy workload of the pathologist. In this study, we have attempted to identify novel molecular markers to find the harboring cancer cells in the lymph node and establish rapid detection method.

Methods: We determined the gene expression profiles of 7 metastatic lymph nodes from patients with OSCC and 1 normal lymph node and 5 salivary glands from non-cancerous patients by microarray analysis. We found the overexpression genes in all metastatic lymph nodes. Subsequently, we examined the expression of these genes in newly 23 metastatic lymph nodes and 9 normal lymph nodes by real-time quantitative RT-PCR (qRT-PCR) assay. Moreover, the rapid detection of lymph node metastasis by these genes was examined using the reverse transcription loop-mediated isothermal amplification (RT-LAMP) method.

Result: Among the 4 genes identified by microarray analysis, annexin A8 (ANXA8) and desmoglein 3 (DSG3) were detected in all metastatic lymph nodes at a much higher level but not in normal lymph nodes at all by qRT-PCR. Furthermore, RT-LAMP method targeting ANXA8 rapidly detected almost lymph nodes with metastasis.

Conclusions: ANXA8 could be a useful marker for detecting lymph node metastasis in OSCC.

overall_design: Using AB1700 system, we determined the gene expression profiles of lymph nodes with metastasis of OSCC. Normal lymph node and salivary gland tissues were used as control samples.


title: Expression profiles of HepG2 cells treated with low-, high-dose of acetaminophen and solvent control

status: Public on Dec 15 2015

city: Maastricht

first: Jian

last: Jiang

address: Maastricht University

department: Toxicogenomics

institute: Maastricht University

summary: The transcriptomics changes induced in the human liver cell line HepG2 by low and high doses of acetaminophen and solvent controls after treatment for 4 time points (12h, 24h, 48h and 72h)

overall_design: The study investigated differential gene expression in HepG2 cell line mRNA following 12 to 72 hours of exposure to low and high doses of acetaminophen and solvent controls. Three biological replicates per compound/solvent.


title: Transcriptome profiling of genetically modified P. falciparum parasite strains with distinct drug resistance phenotypes

status: Public on Dec 09 2015

first: David

last: Fidock

address: 701 W. 168th Street

institute: Columbia University

summary:
We compared the transcriptomic profiles between P. falciparum strains displaying mutant or wild-type pfcrt or varying in pfcrt or pfmdr1 expression levels
All values were normalized using a background pool constituted of 11 transcriptome data sets that constituted a baseline for gene expression fold change and gene set enrichment. In addition to that reported in the present study, the pool included two IDC transcriptome data sets generated for Dd2 parasites pressured long-term with pulses of dihydroartemisinin (the 3b1 line) and the non-pressured parent (Lisewski et al., Cell, 2014), as well as the transcriptome data set previously reported for the 3D7, Dd2 and HB3 strains (Bozdech et al., PLos Biol 2003, Llinas et al, NAR 2006)

overall_design: We conducted gene expression microarrays over the course of the parasite 48-hr IDC, by sampling parasites every 6-hour, representing 8 different time points. Extracted RNA was labeled with Cy5 dye, while the reference RNA pool consisted of Cy3-coupled cDNA samples prepared from RNAs representing all developmental stages at 6-hour intervals of the IDC of the 3D7 line.

first: Sophie

last: Adjalley

first: Daniel

last: Scanfeld

first: Manuel

last: Llinas


title: Time-series of the seed-to-seedling transition in Arabidopsis thaliana

city: Wageningen

first: Anderson Tadeu

last: Silva

state: Gelderland

address: Droevendaalsesteeg 1

department: Plant Physiology

institute: Wageningen University

summary:
The expression levels of Arabidopsis thaliana (Col-0) genes in several developmental stages during the seed-to-seedling transition were measured by using high-density Affymetrix® arrays (Aragene.st1.1).
We used a time-series of microarrays to gain temporal resolution and identify relevant genes in the seed-to-seedling transition.

overall_design: To elucidate the changes in the transcriptome related to the transition from a seed to a photo-autotrophic seedling, seven developmental stages were defined: (DS) mature dry seed; (6h) seeds, imbibed for 6h and germination-related initiation of metabolic activity; (TR), embryo swelling and testa rupture; (RP) protrusion of the radicle through the endosperm, primarily through cell elongation, followed by further embryonic root extension and beginning of (RH) root hair formation, succeed by the appearance of (GC) greening cotyledons and (OC) cotyledons that are fully opened. Three biological replicates represented by pools of seeds bulk-harvested from three to four plants were used.

first: Anderson

middle: T

first: Wilco

last: Ligterink

first: Henk

middle: W

last: Hilhorst


title: AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [Antibody Arrays (L-493)]

city: Boston

first: Ben

middle: S

last: Wittner

address: 185 Cambridge Street

department: Cancer Center

institute: Massachusetts General Hospital

summary: Small-molecule inhibitors of AKT signaling are being in evaluated in patients with various cancer types, but have so far proven therapeutically disappointing for reasons that remain unclear. Here, we treat cancer cells with sub-therapeutic doses of Akti-1/2, an allosteric small molecule AKT inhibitor, in order to experimentally model pharmacologic inhibition of AKT signaling in vitro. We then apply a combined RNA, protein, and metabolite profiling approach to develop an integrated, multi-scale, molecular snapshot of this “AKTlow” cancer cell state. We find that AKT-inhibited cancer cells suppress thousands of mRNA transcripts, and proteins related to the cell cycle, ribosome, and protein translation. Surprisingly, however, these AKT-inhibited cells simultaneously up-regulate a host of other proteins and metabolites post-transcriptionally, reflecting activation of their endo-vesiculo-membrane system, secretion of inflammatory proteins, and elaboration of extracellular microvesicles. Importantly, these microvesicles enable rapidly proliferating cancer cells of various types to better withstand different stress conditions, including serum deprivation, hypoxia, or cytotoxic chemotherapy in vitro and xenografting in vivo. These findings suggest a model whereby cancer cells experiencing a partial inhibition of AKT signaling may actually promote the survival of neighbors through non-cell autonomous communication.

overall_design: Secreted protein profiles of MCF7 and HCT116 Akti-1/2 treated cells and MCF7 and HCT116 vehicle (i.e. DMSO) treated cells were generated using antibody arrays.

first: Xavier

last: Sole

last: Salony

first: Cleidson

middle: P

last: Alves

first: Ipsita

last: Dey-Guha

first: Laila

last: Ritsma

first: Myriam

last: Boukhali

first: Ju

last: Lee

first: Joeeta

last: Chowdhury

first: Kenneth

middle: N

last: Ross

first: Wilhelm

last: Haas

first: Shobha

last: Vasudevan

first: Sridhar

last: Ramaswamy


title: Rader HHDL genotyping

status: Public on Dec 17 2015

city: Philadelphia

first: Daniel

middle: J

last: Rader

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: The presence of a coding variant affecting plasma high density lipoprotein cholesterol (HDLC) levels  was evaluated in subjects with elevated plasma levels of HDLC.

overall_design: 18 DNA samples from subjects with high plasma HDLC levels were analyzed. The samples were analyzed using the exome chip in three separate phases, with different samples in each phase. The same genotyping platform was used for each of the phases of the experiment under the same experimental conditions. Because different samples were run in different phases, raw intensity data was collected separately for each phase and genotypes were called separately for each phase. Raw intensity data is provided thus separately for the subjects by phase of genotyping. The experimental phase of each subject is also provided.

first: Paolo

last: Zanoni

first: Sumeet

last: Khetarpal


title: Chronic binge alcohol administration dysregulates global regulatory gene networks associated with skeletal muscle wasting in simian immunodeficiency virus-infected macaques

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary:
Background: There are more than 1 million persons living with HIV/AIDS (PLWHA) in the United States and approximately 40% of them have a history of alcohol use disorders (AUD). Chronic heavy alcohol consumption and HIV/AIDS both result in reduced lean body mass and muscle dysfunction, increasing the incidence of comorbid conditions. Previous studies from our laboratory using rhesus macaques infected with Simian immunodeficiency Virus (SIV) demonstrated that chronic binge alcohol (CBA) administration in the absence of antiretroviral therapy exacerbates skeletal muscle (SKM) wasting at end-stage SIV disease. The aim of this study was to characterize how CBA alters global gene regulatory networks that lead to SKM wasting at end-stage disease. Administration of intragastric alcohol or sucrose to male rhesus macaques began 3 months prior to SIV infection and continued throughout the duration of study. High-output array analysis was used to determine CBA-dependent changes in mRNA expression, miRNA expression, and promoter methylation status of SKM at end-stage disease (~10 months post-SIV) from healthy control (control), sucrose-administered, SIV-infected (SUC/SIV), and CBA-administered/SIV-infected (CBA/SIV) macaques.
Results: In addition to previously reported effects on the extracellular matrix and the promotion of a pro-inflammatory environment, we found that CBA adversely affects gene regulatory networks that involve universal cellular functions, protein homeostasis, calcium and ion homeostasis, neuronal growth and signaling, and satellite cell growth and survival.
Conclusions: The results from this study provide an overview of the impact of CBA on gene regulatory networks involved in biological functions, including transcriptional and epigenetic processes, illustrating the genetic and molecular mechanisms associated with CBA-dependent SKM wasting at end-stage SIV infection.

overall_design: Animals were exposed to daily intragastric administration of a mean of 2.5 g per kg body weight ethanol (30% w/v water), beginning 3 months prior to SIV infection and continuing throughout the duration of study. Three months later animals were inoculated intravenously with 10,000 times the 50% infective dose (ID50) of SIVmac251. SKM tissues were collected and snap frozen until use.

first: Liz

last: Simon

first: Andrew

last: Hollenbach

first: Patricia

middle: E

last: Molina


title: Comparative analysis of Musculus longissimus dorsi expression of Holstein x Charolais F2 cattle (SEGFAM) with high and low intramuscular fat (IMF) content

status: Public on Dec 02 2015

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

summary: 10 + 10 Holstein x Charolais F2 cattle were assigned to 2 groups with high and low IMF content, respectively; Musculus longissimus dorsi mRNA expression was determined by microarray analysis

overall_design:
pairwise comparison of Affymetrix GeneChip microarray expression profiles of Musculus longissimus dorsi samples derived from crossbred bulls with high and low IMF content
Type: paired t-test

first: Steffen

last: Maak

first: Siriluck

last: Ponsuksili


title: Transcriptional response of muscle tissue to a high energy feeding regimen in Japanese Black and Holstein steers

summary: Microarray gene expression profiling to identify differentially regulated genes in Musculus longissimus dorsi (MLD) of Japanese Black (JB) steers compared to Holstein steers (HS)

overall_design:
pair wise comparison of JB and HS
Type: paired t-test


title: Loss of the proteostasis modulator AIRAPL causes myeloid transformation by deregulating IGF-1 signaling

status: Public on Dec 12 2015

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

institute: Universidad de Oviedo

summary:
Transcriptional profiling of human acute myeloid leukemia cells lines HEL and SET2 transduced with an IGF1R shRNA and miR-125a sponge.

AIRAPL (arsenite-inducible regulatory particle-associated protein-like) is an evolutionarily conserved regulator of cellular proteostasis linked to longevity in nematodes, but whose biological function in mammals is unknown. We show herein that AIRAPL-deficient mice develop a fully-penetrant myeloproliferative neoplastic process. Proteomic analysis of AIRAPL-deficient mice revealed that this protein exerts its antineoplastic function through the regulation of the insulin/IGF-1 signaling pathway. We demonstrate that AIRAPL interacts with newly synthesized insulin-related growth factor-1 receptor (IGF1R) polypeptides, promoting their ubiquitination and proteasome-mediated degradation. Accordingly, genetic and pharmacological IGF1R inhibitory strategies prevent the hematological disease found in AIRAPL-deficient mice as well as in mice carrying the JAK2-V617F mutation, which demonstrates the causal involvement of this pathway in the pathogenesis of myeloproliferative neoplasms. Consistent with its proposed role as a tumor suppressor of myeloid transformation, AIRAPL expression is widely abrogated in human myeloproliferative disorders. Collectively, these findings support the oncogenic relevance of proteostasis deregulation in hematopoietic cells, and unveil novel therapeutic targets for these frequent hematological neoplasias.

overall_design: Human HEL and SET2 cell lines were transduced with IGF1R shRNA and miR-125a sponge, RNA was extracted and transcriptional profiling was obtained with GeneChip Human Gene 2.0 ST Arrays.

first: Fernando

last: Osorio

middle: M

first: Carlos

last: Lopez-Otin


title: Exercise-induced mitochondrial translocation of p53 repairs mitochondrial DNA mutations

status: Public on Dec 11 2015

city: Novato

first: James

last: Flynn

address: 8001 Redwood Blvd.

institute: Buck Institute for Research on Aging

summary: Exercise is a fundamental component of human health that is associated with greater life expectancy and reduced risk of chronic diseases. While the beneficial effects of endurance exercise on human health are well established, the molecular mechanisms responsible for these observations remain unclear. Endurance exercise reduces the accumulation of mitochondrial DNA (mtDNA) mutations, alleviates multisystem pathology, and increases the lifespan of the mtDNA mutator mouse model of aging, in which the proof-reading capacity of mitochondrial polymerase gamma (POLG1) is deficient. Clearly, exercise recruited a POLG1-independent mtDNA repair pathway to induce these adaptations, a novel finding as POLG1 is canonically considered to be the sole mtDNA repair enzyme. Here we investigate the identity of this pathway, and show that endurance exercise prevents mitochondrial oxidative damage, attenuates telomere erosion, and mitigates cellular senescence and apoptosis in mtDNA mutator mice. Unexpectedly, we observe translocation of tumour suppressor protein p53 to mitochondria in response to endurance exercise that facilitates mtDNA mutation repair. Indeed, endurance exercise failed to prevent mtDNA mutations, induce mitochondrial biogenesis, preserve mitochondrial morphology, reverse sarcopenia, and mitigate premature mortality in mtDNA mutator mice with muscle-specific deletion of p53. Our data establish an exciting new role for p53 in exercise-mediated maintenance of the mtDNA genome, and presents mitochondrially-targeted p53 as a novel therapeutic modality for aging-associated diseases of mitochondrial etiology.

overall_design: Microarray analysis of gene expression from skeletal muscle (quadriceps femoris) from Mus musculus. N=23 samples per treatment were analysed for whole transcriptiome gene expression profile using NimbleGen Arrays. The treatment groups included wild-type C57Bl/6J mice as the control group, then two treatment groups which both contained homozygous knock-in mtDNA mutator mice (PolG; PolgAD257A/D257A). Once group of these heterozygous knock out mice received regular endurance exercise sessions while the other group remained sedentraty for 6 months. The control group specimens were wild-type litter mates to the transgenic knockout mice.

first: Adeel

last: Safdar

first: Michael

last: De Lisio

first: Adam

last: Johnston

first: Yevgenya

last: Kratysberg

first: Konstantin

last: Khrapko

first: Imtiaz

middle: A

last: Samjoo

first: Ayesha

last: Saleem

first: Yu

last: Kitaoka

middle: I

last: Ogborn

first: Jonathan

last: Little

first: Sandeep

last: Raha

first: Gianni

last: Parise

first: Mahmood

last: Akhtar

first: Bart

last: Hettinga

first: Glenn

last: Rowe

first: Zoltan

last: Arany

first: Tomas

last: Prolla

first: Mark

last: Tarnopolsky


title: Cross-Platform Assessment of Genomic Imbalance Confirms the Clinical Relevance of Genomic Complexity and Reveals Loci with Potential Pathogenic Roles in Diffuse Large B-Cell Lymphoma

status: Public on Dec 01 2015

city: Rutherford

first: Jane

last: Houldsworth

address: 201 Route 17 North

institute: Cancer Genetics, Inc.

summary: Genomic copy number alterations (CNAs) in diffuse large B-cell lymphoma (DLBCL) have roles in disease pathogenesis but overall clinical relevance remains unclear. Herein, an unbiased algorithm was uniformly applied across three genome profiling datasets comprising 392 newly-diagnosed DLBCL specimens that defined 32 overlapping CNAs, involving 36 minimal common regions (MCRs). Scoring criteria were established for 50 aberrations within the MCRs while considering peak gains/losses. Application of these criteria to independent datasets revealed novel candidate genes with coordinated expression, such as CNOT2, potentially with pathogenic roles. No one single aberration significantly associated with patient outcome across datasets, but genomic complexity, defined by imbalance in more than one MCR, significantly portended adverse outcome in two of three independent datasets. Thus, the standardized scoring of CNAs currently developed can be uniformly applied across platforms, affording robust validation of genomic imbalance and complexity in DLBCL and overall clinical utility as biomarkers of patient outcome.

overall_design: Two-condition experiment, Test DLBCL specimens vs. Reference human genome DNA equimixture of normal male and normal female.

first: Venkata

last: Thodima


title: Hepatic premalignant alterations triggered by human carcinogen aristolochic acid I in canines

city: Hangzhou

first: Kunkai

last: Su

address: 79 Qingchun Road

institute: Zhejiang University

summary: Ten-month-old male beagle canines were purchased from the ANNIMO Science and Technology Ltd (Nanjing, China, Certificate No. SCXK (Su) 2010-0002), and maintained in a specific pathogen-free environment. Canines were randomly assigned to two groups (4 in each group) and received capsules with control filler or Aristolochic Acid I (AAI) filler (3 mg/kg/day, equivalent dose of mouse) for 10 days. Canines were sacrificed at 11 days after initiation of the treatment. Livers were excised immediately after sacrifice. Part of the livers were immediately snap-frozen in liquid nitrogen and kept at -80°C for total RNA isolation and microRNA microarray analysis.

overall_design: In this study, liver samples from eight canines were used to acquire the miRNA expression profiling and the function of the abudant miRNAs were analyzed by bioinformatic methods. AAI-induced dysregulation of let-7 and miR-23a clusters were closely associated with c-Myc and IL-6R signaling.

first: Ke

last: Jin

first: Tong

last: Li

first: Xiaqing

last: Zhu

first: Qi

last: Wang

first: Renshan

last: Ge

first: Zongfu

last: Pan

first: Bowen

last: Wu

first: Lijun

first: Danyan

first: Yihan

last: Zhang

first: Yifan

first: Guofang

last: Shen

first: Chunsheng

last: Xiang

first: Lanjuan

first: Yijia

last: Lou


title: Brain transcriptomic response to social eavesdropping in zebrafish

status: Public on Dec 13 2015

city: Oeiras

first: Joao

middle: Sollari

last: Lopes

address: Rua da Quinta Grande N6

country: Portugal

institute: IGC

summary:
Public information is widely available at low cost to animals living in social groups. For instance, bystanders may eavesdrop on signaling interactions between conspecifics and use it to adapt their subsequent behavior towards the observed individuals. This social eavesdropping ability is expected to require specialized mechanisms such as social attention, which selects social information available for learning. To begin exploring the genetic basis of social eavesdropping, we used a previously established attention paradigm in the lab to study the brain gene expression profile of male zebrafish in relation to the attention they have paid towards conspecifics involved or not involved in agonistic interactions. Microarray gene chips were used to characterize their brain transcriptomes based on differential expression of single genes and gene sets. These analyses were complemented by promoter region-based techniques. Using data from both approaches, we further drafted protein interaction networks. Our results suggest that attentiveness towards conspecifics, whether interacting or not, activates pathways linked to neuronal plasticity and memory formation. The network analyses suggested that fos and jun are key players on this response, and that npas4a, nr4a1 and egr4 may also play an important role.
Furthermore, specifically observing fighting interactions further triggered pathways associated to a change in the alertness status (dnajb5) and to other genes related to memory formation (btg2, npas4b), which suggests that the acquisition of eavesdropped information about social relationships activates specific processes on top of those already activated just by observing conspecifics.

overall_design: 39 fish were previously subjected to one of three treatments (13 individuals per group) for 30 minutes: bystander to an interacting male conspecific dyad; bystander to two non-interacting male conspecifics; and socially isolated fish. From these, 4 representative groups (each composed of 3 replicates) were selected for total RNA expression analyses: one attentive group from the interacting-conspecifics treatment; two groups from the non-interacting-conspecifics treatment, based on attentive and inattentive behavioral profiles; and one group from the isolated fish to be used as a reference.

first: Lopes

last: Joao

first: Abril-de-Abreu

last: Rodrigo

first: Oliveira

middle: F

last: Rui


title: microRNA expression in lung squamous cell carcinoma cell lines

city: Macclesfield

first: Molly

middle: Ann

last: Taylor

address: 33F83 Mereside, Alderley Park

country: United Kingdom

institute: AstraZeneca

summary: microRNA expression data from AstraZeneca internal  squamous cell carcinoma cell line panel

overall_design: 15 Samples representing 14 cell lines.

first: Mark

last: Wappett

first: Oona

last: Delpuech

first: Helen

last: Brown

first: Christine

last: Chresta


title: Comparison of gene expression by sheep and human blood stimulated with the TLR4 agonists lipopolysaccharide and monophosphoryl lipid A [sheep]

status: Public on Dec 16 2015

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary:
11,431 and 4,992 genes were determined in whole blood of healthy human volunteers and normal sheep, respectively following MPLA and LPS exposure
Following the exposure 1,029 human and 175 sheep genes were differentially expressed. Of those 175 sheep genes, 54 had a known human ortolog. The major inflammatory mediators, such as IL-1-6-8, TNFa, NFkB, ETS2, PTGS2, PTX3, CXCL18, KYNU, and CLEC4E were similarly (>2-fold) upregulated in both human and sheep blood.

overall_design: Six healthy human volunteers and six normal sheep blood was incubated with LPS or MPLA for 90 minutes, then the blood was transferred to the Paxgene blood RNA tubes and the gene expression microarrays were scanned with G2556 Microaaray Scanner

first: Perenlei

last: Enkhbaatar

first: Christina

last: Nelson

first: John

last: Salsbury

first: Joseph

middle: R

last: Carmical

first: Karen

last: Torres

first: David

last: Herndon

first: Donald

last: Prough

first: Liming

last: Luan

first: Edward

last: Sherwood


title: Targets of the small regulatory RNA DapZ

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: To determine the targets of the small regulatory RNA DapZ in S. Typhimurium, we looked at the effect of a short pulse of DapZ over-expression on the Salmonella transcriptome, as well as a DapZ variant that lacks the GcvB-like R1 region. To achieve over-expression, the wild-type DapZ and its variant were cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. A strain carrying the pBAD plasmid w/o insert was used as negative control (also induced by L-arabinose). 2 biological replicates were performed. This sRNA target identification strategy has been described in Papenfort et al; Molecular Microbiology (2006) 62(6), 1674-1688.

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

overall_design: We used whole-genome S. typhimurium microarrays to determine relative mRNA expression changes, comparing the mRNA profiles. Microarrays used in this study were produced by in-situ synthesis as 8x15k multipack format from Agilent Technologies. Each microarray comprises 13268 60-mer S. typhimurium strain SL1344 specific oligonucleotides supplemented with 319 60-mer S. enterica subsp. serovar Typhimurium 14028S specific oligonucleotides, 360 60-mer S. typhimurium LT2 specific oligonucleotides and 360 60-mer oligonucleotides specific for 149 Salmonella sRNAs. The experimental design involves the use of Salmonella enterica serovar Typhimurium genomic DNA as the co-hybridized control for one channel on all microarrays. Two independent biological eperiments were analyzed.

first: Yanjie

last: Chao

first: Kai

last: Pappenfort

first: Jörg

last: Vogel


title: A microarray-based analysis of oocytes quality of the European clam Ruditapes decussatus

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

country: Italy

institute: University of Padova

summary: The European clam, Ruditapes decussatus (Linnaeus, 1758) is a bivalve mollusc of the family Veneridae native to the European Atlantic and Mediterranean coastal waters. Its production is exclusively based on natural recruitment, which is subject to high annual fluctuations due to adversely affected by pollution and other environmental factors. A microarray-based analysis was performed with the objectives of describe genomic feature of oocytes and identify potential markers of oocyte quality in the economically important European clam, Ruditapes decussatus. The oocytes of a total of 25 females from Ria de Aveiro, Western coast of Portugal, were selected for this study and their quality was estimated by early developmental success until D-larval rate, under controlled conditions.

overall_design: Clams (Ruditapes decussatus) were induced to spawn, in four different dates, by thermal stimulation, with temperature increasing from 5 to 28 ± 1 °C. To avoid uncontrolled fertilization, females once identified were stored in individual containers for spawning. From each female, three samples of 20 000 oocytes were taken.  For RNA-sequencing and microarray analysis, total RNA was isolated on 25 oocyte samples collecting from 25 clam females 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 R.decussatus oligo-DNA microarray of 59,951 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA at a resolution of 2 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. FeatureExtraction v10.7.3.1 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Luca

last: Bargelloni

first: Marianna

last: Pauletto

first: Arnaud

last: Huvet

first: Joana

last: Teixeira de Sousa


title: Effects of an adrA mutant on Salmonella enterica gene expression during root colonization

status: Public on Dec 04 2015

city: Madison

first: Kimberly

last: Cowles

state: WI

address: 1630 Linden Drive

institute: University of Wisconsin-Madison

summary: Increasing evidence indicates that despite exposure to harsh environmental stresses, Salmonella enterica successfully persists on plants, utilizing fresh produce as a vector to animal hosts. This study examined the mechanisms of S. enterica plant colonization, including the role of the diguanylate cyclase AdrA. Utilizing microarray analysis, we identified a new function for AdrA in the transcriptional regulation of colanic acid biosynthesis genes.

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

overall_design: Changes in gene expression, comparing wildtype to an adrA mutant, were measured in planktonic bacterial cells after 24-hour incubation with alfalfa seeds.  Two independent experiments were performed for each strain (wildtype and the adrA mutant).

first: K

first: J

middle: D

last: Barak


title: Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown

status: Public on Dec 10 2015

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

summary:
Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease.
In this data set, we included the data from microarray experiments.

overall_design: We performed microarray analysis to profile gene expression and splicing changes in mouse hippocampal cultures (14 DIV) with Rbfox1 and Rbfox3 double knockdown by siRNAs. Before the treatment of siRNAs, the hippocampal cultures were treated with AraC to eliminate glial cells and co-cultured with cortical cultures to support the growth of neurons. Six samples were analyzed.

first: Ji-Ann

last: Lee

first: Chia-Ho

first: Erik

last: Anderson

first: Douglas

last: Black

first: Kelsey

middle: C

last: Martin


title: Cryptococcus neoformans gene expression in minimal media of wild type (WT) and all1all2Δ mutant cells

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: To examine the comparative transcription profile of WT and all1all2Δ mutant cells in in vitro conditions to determine genes resposible for hyporvirulent phenotype of all1all2Δ mutant cells. Using transcriptional profiling, we determined that many genes involved in amino acid transport were differentially transcribed between the wild type and the all1all2Δ mutant strain. The genes differentially expressed in double mutant of ALL1 ALL2 did not overlap with ALL1 and ALL2 comparative transcriptomes with RC2 (WT).

overall_design: For arrays, total RNA was isolated from WT and all1all2Δ mutant using Qiagen RNeasy Kit. For RNA extraction, WT and all1all2Δ mutant were grown in minimal media. Cells were grown for overnight, diluted 1:100 and then again grown overnight or up to an OD of 0.6-0.7 with agitation (150rpm) at 37°C.

first: Neena

last: Jain

first: Bettina

last: Fries


title: Cryptococcus neoformans gene expression in minimal media of wild type (WT) and ALL2 mutant (all2Δ) cells

summary: To examine the comparative transcription profile of WT and all2Δ mutant cells in in vitro conditions to determine genes responsible for hypervirulent phenotype of all2Δ cells. Using transcriptional profiling, we determined that many genes involved in transport were differentially transcribed between the wild type and the mutant strain. With the help of further experiments we could rule out that ALL2 has a unique function in maintaining the intracellular pH under acidic conditions.

overall_design: For arrays, total RNA was isolated from WT and all2Δ mutant using Qiagen RNeasy Kit. For RNA extraction, WT and all2Δ mutant were grown in minimal media. Cells were grown for overnight, diluted 1:100 and then again grown overnight or up to an OD of 0.6-0.7 with agitation (150rpm) at 37°C.


title: Transcriptional responses of Pseudomonas veronii 1YdBTEX2 to the exposure to laboratory induced matric and solute stresses

city: Lausanne

first: Silvia

middle: K.

last: Moreno-Forero

state: Vaud

address: Batiment Biophore, Unil Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

summary: We study the transcriptional reactions of bacteria interesting for biodegradation under laboratory conditions that mimic water stress. We compared the transcriptomes of cultures growing exponential phase under optimal conditions versus their responses to an osmotic shock of 30 min in exponential phase. The osmotic shock consisted in a reduction of water potential induced by salt (NaCl, solute stress) or by polyethylene glycol (PEG8000, matric stress). The stress was such that cells are not more than 20% affected in their maximum growth rate.

overall_design: The purpose of this study is to compare the responses of Pseudomonas veronii 1YdBTEX2 under solute and matric shock stresses (30min of exposition). These transcriptome responses will be compared with those experiences by other strain potentially useful for bioremediation in order to understand better their behaviour in inoculations in soil.

middle: K

first: Jan

last: van der Meer


title: Analysis of a novel existence region of Sir3p in S. cerevisiae

status: Public on Nov 18 2015

city: Fukui

first: Kay

last: Taniguchi

state: Fukui

address: 3-9-1, Bunkyo

institute: University of Fukui

type: Genome binding/occupancy profiling by genome tiling array

summary: In the budding yeast, HMR, HML, telomere and rDNA domain are known as a silencing region. Sir2 need to make it at rDNA and, HMR, HML and the telomere need to Sir2, Sir3, Sir4 complex to control internal gene repression. In this report, we found a newly Sir3 binding domain, CN domain (Chromosome New region) 1~14, by the ChIP on chip analysis on S.cerevisiae chromosome. In addition, we also performed ChIP on chip analysis with anti-Sir3 antibody using G1 phase synchronized cell to find Sir3 distribution difference of stage of cell cycle and we found CN15~CN25 which was G1 phase specific Sir3 binding region. Furthermore, we analyzed difference of gene expression at CN region in sir3 strain, and some regions did not change level of gene expression. In the conventional report, Sir3 had recruited by Sir2 and Sir4 on chromosome, but recruit of Sir3 was independent on Sir2 and Sir4 at some CN regions. These data suggested that we found a newly Sir3 function and Sir3 recruited system on chromosome.

overall_design: Distribution of Sir3 on chromosomes during log phase or G1 phase. In the both cases, hybridization data for ChIP fraction was compared with Input (whole cell extract fraction). Several binding signals were confirmed by quantitative real time PCR.

first: Risa

last: Mitsumori

first: Tomoe

last: Ohashi

first: Kazuto

last: Kugou

first: Ayako

last: Ichino

first: Kei

first: Kunihiro

last: Ohta

first: Hiroyuki

last: Uchida

first: Masaya

last: Oki


title: Comparative transcriptome analysis of Brassica napus L. male sterility induced by the Chemical Hybridization Agent Monosulfuron Ester Sodium

status: Public on Dec 05 2015

city: Fuzhou

first: Zhanjie

last: Li

state: Fujian

address: No.15 Shangxiadian Road

department: College of Crop Science

institute: Fujian Agriculture and Forestry University

summary: Chemical hybridization agent (CHA)-induced male sterility is becoming one of the most useful tools for the crop heterosis in seed production. We had previously discovered monosulfuron ester sodium (Mes), an acetolactate synthase (ALS) inhibitor of the herbicide sulfonylurea family, could induce rapeseed (Brassica napus  L.) male sterility. To investigate the mechanism of Mes inducing male sterility, a cytological analysis and comparative transcriptome analysis were performed between Mes-treated plants leaves and different developmental stage anthers and those of the Mock-treated plants. Cytological analysis exhibited that Mes destroyed plastids ultrastructure and depressed the materials accumulation during anther development and maturation process. Comparative transcriptome analysis identified a total of 1501 transcripts differentially expressed in the leaves and different developmental stage anthers. Subcellular localization analysis, functional analysis and pathway analysis were carried out to obtain the clues that plastid was the seriously damaged organelle, and many genes involved in carbon and lipid metabolism and cellular transport differentially expressed. Detailed expression pattern analysis of genes related with these functions were conducted and verified by RT-PCR. In addition, several transcription factors, protein kinases and hormone related genes were identified. Carbohydrate content analysis confirmed carbon metabolism were influenced by Mes. Taken together, we proposed a putative action mode that Mes inhibited activity of acetolactate synthase, which localized in plastid in plants, and then disturbed the normal supply of carbon and lipid metabolite for anther development, finally displayed male sterility. This results have important significance for uncovering the metabolic gene regulation during anther development and may provide more potential targets for developing new male sterility inducing CHAs in rapeseed breeding.

overall_design: Rapeseed (Brassica napus L.) plants were foliar sprayed with 0.1μg mL-1 Monosulfuron ester sodium (Mes) solution containing 50ppm DMF and 5ppm Tween 80 for about 15 ml per plant. Young leaves (C2Y1, C2Y2, C2Y3; T2Y1, T2Y2, T2Y3) of the main inflorescences and developing anthers (including small buds (C2S1, C2S2, C2S3; T2S1, T2S2, T2S3), middle anthers (C2M1, C2M2, C2M3; T2M1, T2M2, T2M3), and large anthers (C2L1, C2L2, C2L3; T2L1, T2L2, T2L3)) from Mes-treated and Mock-treated plants were collected for each experiment. Each tissue has three independent biological replicates.

first: Yufeng

last: Cheng

first: Jianmin

last: Cui

first: Peipei

last: Zhang

first: Peng

last: Zhou

first: Huixian

last: Zhao

first: Shengwu

last: Hu


title: AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [Antibody Arrays (L-507)]

city: Boston

first: Ben

last: Wittner

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Small-molecule inhibitors of AKT signaling are being in evaluated in patients with various cancer types, but have so far proven therapeutically disappointing for reasons that remain unclear. Here, we treat cancer cells with sub-therapeutic doses of Akti-1/2, an allosteric small molecule AKT inhibitor, in order to experimentally model pharmacologic inhibition of AKT signaling in vitro. We then apply a combined RNA, protein, and metabolite profiling approach to develop an integrated, multi-scale, molecular snapshot of this “AKTlow” cancer cell state. We find that AKT-inhibited cancer cells suppress thousands of mRNA transcripts, and proteins related to the cell cycle, ribosome, and protein translation. Surprisingly, however, these AKT-inhibited cells simultaneously up-regulate a host of other proteins and metabolites post-transcriptionally, reflecting activation of their endo-vesiculo-membrane system, secretion of inflammatory proteins, and elaboration of extracellular microvesicles. Importantly, these microvesicles enable rapidly proliferating cancer cells of various types to better withstand different stress conditions, including serum deprivation, hypoxia, or cytotoxic chemotherapy in vitro and xenografting in vivo. These findings suggest a model whereby cancer cells experiencing a partial inhibition of AKT signaling may actually promote the survival of neighbors through non-cell autonomous communication.

overall_design: Secreted protein profiles of MCF7 and HCT116 Akti-1/2 treated cells and MCF7 and HCT116 vehicle (i.e. DMSO) treated cells were generated using antibody arrays.

first: Xavier

last: Sole

last: Salony

first: Cleidson

last: Alves

first: Ipsita

last: Dey-Guha

first: Laila

last: Ritsma

first: Myriam

last: Boukhali

first: Ju

middle: H

last: Lee

first: Joeeta

last: Chowdhury

first: Kenneth

last: Ross

first: Wilhelm

last: Haas

first: Shobha

last: Vasudevan

first: Sridhar

last: Ramaswamy


title: Transposon sequencing during experimental osteomyelitis reveals hypoxic responses as key components of the staphylococcal-host interaction

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
The Staphylococcus aureus two-component regulatory system, SrrAB, coordinates hypoxic responses during in vitro growth conditions.
S. aureus Affymetrix GeneChips were used to compare S. aureus expression properties of wild type and isogenic ssrA mutant cells during aerobic growth conditions.
S. aureus Affymetrix GeneChips were also used to compare the S. aureus expression properties of wild type and isogenic ssrA mutant cells during hypoxic growth conditions.
Few differences were observed between the expression properties of S. aureus wildtype and ssrA mutant cells during aerobic growth.
Significant differences were observed between the expression properties of S. aureus wild type and ssrA mutant cells during hypoxic growth.

overall_design: S. aureus strain USA300 (wild type) or an isogenic srrAB mutant (DssrA) were grown in laboratory medium to exponential under aerobic or hypoxic growth conditions, total bacterial RNA was isolated, labeled and applied to Affymetrix GeneChips.  We sought to determine whether the transcriptional profiles of S. aureus wild type and ssrAB mutant cells differed during aerobic and hypoxic growth conditions.

first: James

last: Cassat


title: The role of viral microRNAs in Burkitt Lymphoma: the Epstein Barr-encoded Bart-6-3p microRNA regulates cell proliferation and immunosurveillance

status: Public on Nov 30 2015

city: Santander

first: Lorena

last: Di Lisio

address: Avda Cardenal Herrera Oria s/n

institute: IFIMAV

summary: Compare Epstein-Barr-positive and Epstein-Barr-negative Burkitt lymphoma cases forboth cellular and viral microRNA expression profile, and to assess the role of viralmicroRNAs in Burkitt lymphomagenesis

overall_design: 12 samples of EBVnegative Burkitt Lymphoma has been compared vs. 6 samples of EBVpositive Samples

first: Maria

last: Rm Ambrosio

first: Mohsen

last: Navari

first: Eduardo

middle: a

last: Leon

first: Anna

last: Onnis

first: Cristina

last: Ulivieri

first: Gonzalo

last: Gomez

first: Stefano

last: Lazzi

first: Miguel

last: Piris

first: Lorenzo

last: Leoncini

first: Giulia

last: De Falco


title: Effects of High Hydrostatic Pressure on Expression Profiles of In Vitro Produced Vitrified Bovine Blastocysts

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: High hydrostatic pressure (HHP) has been used to pre-condition embryos before essential, yet potentially detrimental procedures such as cryopreservation. However, the mechanisms for HHP are poorly understood. We treated bovine blastocysts with three different HHP (40, 60 and 80 MPa) in combination with three recovery periods (0, 1h, 2h post HHP). Re-expansion rates were significantly higher at 40 and 60 but lower at 80 MPa after vitrification-warming in the treated groups than controls. Microarray analysis revealed 399 differentially expressed transcripts, representing 254 unique genes, among different groups. Gene ontology analysis indicated that HHP at 40 and 60 MPa promoted embryo competence through down-regulation of genes in cell death and apoptosis, and up-regulation of genes in RNA processing, cellular growth and proliferation. In contrast, 80 MPa up-regulated genes in apoptosis, and down-regulated protein folding and cell cycle-related genes. Moreover, gene expression was also influenced by the length of the recovery time after HHP. The significantly over-represented categories were apoptosis and cell death in the 1h group, and protein folding, response to unfolded protein and cell cycle in the 2h group compared to 0h. Taken together, HHP promotes competence of vitrified bovine blastocysts through modest transcriptional changes.

overall_design: 4*3*2 design experiment. The following treatments were included: (1) Control embryos were left untreated in the incubator (one atmospheric pressure or 0.1 MPa); (2) treatment groups were assigned to 40, 60 and 80 MPa HHP for 1h at either 24°C (room temperature) or 39°C (body temperature), followed by three different recovery time periods (0, 1 and 2h) post-HHP in the holding medium. Biological replicates: 3 control replicates. Technical replicates: dye-swap.

first: Patrick

last: Harrington

first: Ming

last: Zhang

first: Sadie

middle: L

last: Marjani

first: Joonghoon

last: Park

first: Lynn

last: Kuo

first: Csaba

last: Pribenszky

first: Xiuchun

last: Tian


title: Dose and Effect Thresholds for Early Key Events in a PPARα Tumorigenic Mode of Action

status: Public on Nov 03 2015

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

institute: US EPA

summary:
The goal of this study was to determine short-term key event markers using qualitative and quantitative methods in an established pathway of mouse liver tumorigenesis mediated by peroxisome proliferator-activated receptor alpha (PPARα).
a 7-day case study approach was used to determine transcriptional PODs and effect thresholds for early key events in an established MOA for liver tumorigenesis in mice.  The target pathway is mediated by peroxisome proliferator-activated receptor alpha (PPARalpha) (Corton et al. 2013). In this study we analyzed three reference phthalates with different levels of receptor activity and liver outcomes at 2 years.

overall_design:
In this study we analyzed three reference phthalates with different levels of receptor activity and liver outcomes at 2 years.
Male B6C3F1 mice were exposed for 7 days to three reference phthalates, di(2-ethylhexyl) phthalate (DEHP), di-n-octyl phthalate (DNOP), and n-butyl benzyl phthalate (BBP), with a range of PPARα activation and tumorigenic potential (DEHP>BBP>DNOP) and phenobarbital(PB). Each phthalate resulted in increased target gene expression associated with PPARα activation, while only DEHP showed significant hepatocellular proliferation assessed by Ki67 labeling index (LI).
A total of 77 samples were analyzed.  4 reps per group.

first: April

last: Lake

first: Charles

last: Wood

first: Virunya

middle: S

last: Bhat

first: Brian

middle: N

last: Chorley

first: Gleta

last: Carswell

first: Yusupha

last: Sey

first: Elaina

last: Kenyon

first: Beth

last: Padnos

first: Tanya

last: Moore

first: Alan

last: Tennant

first: Judith

last: Schmid

first: Barbara

last: George

first: David

middle: G

last: Ross

first: Micheal

last: Hughes

first: J

last: Corton

first: Jane

last: Simmons

first: Charlene

last: McQueen


title: Human Exon 1.0 ST Affymetrix array data from SHSY-5Y cells

city: Bristol

first: James

last: Uney

address: Medical School, University Walk

department: School of Clinical Sciences

institute: University of Bristol

summary: Comparison of control vs SAFB1 knockdown

overall_design: 6 samples were analysed (3 control vs 3 siSAFB1 knockdown) by AltAnalyze

first: Caroline

last: Rivers


title: long non-coding RNA expression profiles in Paraquat-induced pulmonary fibrosis

status: Public on Oct 06 2015

city: Nanjing

first: HAO

last: SUN

state: Jiangsu

address: Guangzhou Road 300

department: Department of Emergency

institute: The first affiliated hospital with Nanjing Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, using the next generation transcriptome sequencing and microarray analysis, we profiled expression of long non-coding RNAs (lncRNAs) in a mouse model of paraquat-induced pulmonary fibrosis. We identified 513 up-regulated and 204 down-regulated lncRNAs (fold-change ≥5.0) when comparing fibrotic to normal lung tissues. Quantitative real-time PCR, Gene Ontology analysis, Pathway analysis and Bioinformatics analysis were performed for further research. Furthermore, we predicted and verified the target genes of two up-regulated lncRNAs, uc.77 and 2700086A05Rik, as Zeb2 and Hoxa3 respectively, both of which are important regulators of EMT.

overall_design: BALB/c mice (7-8 weeks, male, 19.8 g±0.63 g) were provided by Experimental Animal Center of Nanjing Medical University, China. A total of 20 BALB/c mice were randomly divided into 2 groups (n=10 in each group): the normal control and pulmonary fibrosis model group. Mice in the model group were administered 10mg/kg paraquat (SIGMA Chemical Co., St. Louis, MO, USA) dissolved in sterile saline via intraperitoneal injection (once per day for 5 days). The normal control group were administered an equal volume of saline at the same time. Lung tissues were harvested on the 12st day following the first treatment. The motality of paraquat group was 70%. Three lung tissues from each group were pick up and mixed to prepare for the RNA extraction and the following microarray analysis.

first: Hao

last: Sun

first: Jinsong

last: Zhang

first: Junjie

last: Chen


title: Transcriptional responses of Arthrobacter chlorophenolicus to the exposure to laboratory induced matric and solute stress

first: Silvia

last: Moreno-Forero

overall_design: The purpose of this study is to compare the responses of Arthrobacter chlorophenolicus A6 under solute and matric shock stresses (30min of exposition). These transcriptome responses will be compared with those experiences by other strain potentially useful for bioremediation in order to understand better their behaviour in inoculations in soil.

first: Jan

last: van der Meer


title: Copy number analysis of DCIS with and without recurrence

city: East Melbourne

first: Kylie

last: Gorringe

state: Victoria

address: St Andrew's Pl

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

summary: We analysed a cohort of pure DCIS cases treated only with wide local excision for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan® MIP arrays. Cases included those without recurrence within 6 years (n=25) and with recurrence between 1-5 years after diagnosis (n=15). Additional cases were excluded for low grade (n=6) or non-clonal recurrence (n=2). Recurrence tumour was available for 8 cases. Pure DCIS were broadly similar in copy number changes compared to invasive breast cancer, with the consistent exception of a greater frequency of ERBB2 amplification in DCIS. There were no significant differences in age or ER status between the cases with a recurrence versus those without. Overall, the DCIS cases with recurrence had more copy number events than the DCIS without recurrence. The increased copy number appeared non-random with several genomic regions showing an increase in frequency in recurrent cases including 20q gain, ERBB2 amplification and 15q loss. Copy number changes may provide prognostic information for DCIS recurrence but validation in additional cohorts is required.

overall_design: 48 cases of synchronous DCIS and IDC were microdissected from FFPE tissue and analysed by molecular inversion probe (MIP) copy number arrays. The arrays were a mixture of early and later release OncoScan arrays and the data for early release cases in this submission are CN values for the ~300,000 probes common to two batches performed. Raw data is retained by Affymetrix.


title: Gene expression pattern of Arabidopsis (WT and wrky6) colonized with Piriformospora indica under low and normal phosphate conditions

status: Public on Nov 28 2015

city: Jena

first: Madhunita

last: Bakshi

address: Dornburger Str. 159

department: Plant physiology

institute: Friedrich-Schiller Universität Jena

summary: A whole cascade of genes involved in abiotic stress tolerance, starting from stress perception to transcriptional activation of downstream genes, leads to stress adaptation and tolerance responses in Arabidopsis. Understanding the function of their gene products is of critical importance for the development of transgenic strategies and to improve stress tolerance in crops. Pi limitation is one of the major abiotic stresses for plants used in agriculture. Using Arabidopsis as a model system, we provide evidence that WRKY6 functions as a repressor of several Pi-related processes in LP-exposed Arabidopsis roots, among them Pi transporter and metabolism genes. Inactivation of WRKY6 stimulates the Pi uptake and metabolism in LP-exposed WT roots. The Pi metabolism is further promoted by P. indica under Pi limitation conditions and the stimulatory effect of the fungus is much stronger in the wrky6 background when compared to the WT. Better performance of P. indica-colonized WT and mutant plants under Pi limitations is manifested by the healthy phenotype of the plants and growth promotion of their underground and aerial parts. In the wrky6 background, this results in larger roots with a bushy phenotype. It allows the identification of genes and mechanisms which trigger root growth and development as well as the alteration of the root architecture for optimal performance in the rhizospheric environment.

overall_design: Low phosphate induced gene expression in Arabidopsis (WT and wrky6) was measured at 3dpi from P. indica colonized and uncolonized seedlings after exposure to 0.25mM, LP and 2.5mM, NP. Three independent experiments were performed.


title: Identification of AP2-O targets [microarray]

status: Public on Jun 01 2015

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

summary: Stage-specific transcription is a fundamental biological process in the lifecycle of the Plasmodium parasite. Proteins containing the AP2 DNA-binding domain are responsible for stage-specific transcriptional regulation, and belong to the only known family of transcription factors in Plasmodium parasites. A comprehensive identification of their target genes will advance our understanding of the molecular basis of stage-specific parasite development. In this study, we have used ChIP-seq technology to identify the target genes of the ookinete-specific AP2 transcription factor AP2-O.

overall_design: Five biologically independent AP2-O(−) and seven biologically independent wild-type ookinete samples were used in the analyses.

first: Masao

last: Yuda

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Tomomi

last: Kato


title: The identification of miRNA biomarkers in CFS/ME peripheral blood samples

status: Public on Oct 01 2015

city: London

first: Robert

middle: Daniel

last: Petty

address: Charterhouse Square

department: Haemato-oncology

institute: Barts Cancer Institute, Queen Mary, University of London

summary: Chronic Fatigue Syndrome (CFS/ME) is a complex multisystem disease, with a pathogenesis that is undetermined. A large cohort of genes demonstrating altered expression in CFS/ME implicates the role of translational regulatory molecules, microRNA (miRNA), in the pathogenesis of this disease. We aimed to define the changes in microRNA expression in peripheral blood mononuclear cell (PBMC) samples in CFS/ME patients. miRNA expression was analysed in PBMC samples taken from CFS/ME patients and healthy controls, using the Ambion Bioarray V1. miRNA demonstrating differential expression were validated by qRT-PCR and analysed in an independent patient cohort in fractionated blood cell populations. The targets of miRNA hsa-miR-99b and hsa-miR-330-3p were then identified by gene expression analysis after transfection into primary NK cells.Microarray analysis identified differential expression of 34 miRNA, all of which were up-regulated. Four of the 34 miRNA had confirmed expression changes by qRT-PCR. Fractionating PBMC samples by cell type from an independent patient cohort identified changes in miRNA expression in NK-cells, B-cells and monocytes with the most significant abnormalities occurring in NK cells. Transfecting primary NK cells with hsa-miR-99b and hsa-miR-330-3p, respectively, resulted in gene expression changes consistent with NK cell activation and diminished cytotoxicity.This study demonstrates altered microRNA expression in the peripheral blood mononuclear cells of CFS/ME patients, which are potential diagnostic biomarkers. The greatest degree of miRNA deregulation was identified in NK cells with targets consistent with cellular activation and altered effector function.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Total RNA was isolated from PBMC samples obtained from blood samples taken from patients with an established diagnosis of CFS/ME (n=15) and age and sex matched healthy donors (n=30). Duplicate samples were prepared for 7 samples (P100, P103-P108) as technical replicates. Samples P100_1 and C261 failed hybridization quality control and were excluded.


title: Rad53-mediated regulation of Rrm3 and Pif1 DNA helicases contributes to prevention of aberrant fork transitions under replication stress.

status: Public on Sep 24 2015

city: Milano

first: Michele

last: Giannattasio

state: Italy

address: Via Adamello, 16

department: Genome stability

institute: IFOM

summary: Replication stress activates the Mec1ATR and Rad53 kinases. Rad53 phosphorylates nuclear pores to counteract gene gating, thus preventing aberrant transitions at forks approaching transcribed genes. Here, we show that Rrm3 and Pif1, DNA helicases assisting fork progression across pausing sites, are detrimental in rad53 mutants experiencing replication stress. Rrm3 and Pif1 ablations rescue cell lethality, chromosome fragmentation, replisome-fork dissociation, fork reversal, and processing in rad53 cells. Through phosphorylation, Rad53 regulates Rrm3 and Pif1; phospho-mimicking rrm3 mutants ameliorate rad53 phenotypes following replication stress without affecting replication across pausing elements under normal conditions. Hence, the Mec1-Rad53 axis protects fork stability by regulating nuclear pores and DNA helicases. We propose that following replication stress, forks stall in an asymmetric conformation by inhibiting Rrm3 and Pif1, thus impeding lagging strand extension and preventing fork reversal; conversely, under unperturbed conditions, the peculiar conformation of forks encountering pausing sites would depend on active Rrm3 and Pif1.

overall_design: BrdU incorporation profiles by ssDNA-BrdU IP on chip have been generated as described (Katou et al., 2003). Protein binding profiles by ChIP-chip  analysis were generated as described (Bermejo et al., 2009). Labeled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

middle: E

last: Rossi

first: Marco

last: Foiani


title: Toxoplasma gondii arginine methyltransferase 1 (PRMT1) regulates parasite counting during tachyzoite cell division

status: Public on Sep 18 2015

city: Tampa

first: Elena

last: Suvorova

state: Florida

address: 3720 Spectrum Blvd

department: Internal Medicine

country: USA

institute: University of South Florida

summary:
PRMT1 is thought to be responsible for the majority of PRMT activity in Toxoplasma gondii, but its exact function is unknown. We generated T. gondii mutants lacking PRMT1 (∆prmt1) by deletion of the PRMT1 gene. ∆prmt1 parasites exhibit morphological defects during cell division and grow slowly, and this phenotype reverses in the complemented strain ∆prmt::PRMT1mRFP.  PRMT1 localizes primarily in the cytoplasm with enrichment at the centrosome, and the strain lacking PRMT1 is unable to segregate progeny accurately. Unlike wild-type and complemented parasites, ∆prmt1 parasites have abnormal daughter buds, perturbed centrosome stoichiometry, and loss of synchronous replication.
Whole genome expression profiling demonstrated differences in expression of cell cycle regulated genes in ∆prmt1 relative to the complemented ∆prmt1::PRMT1mRFP and parental wild-type strains, but these changes did not correlate with a specific block in cell cycle. Although PRMT1’s primary biological function was previously proposed to be methylation of histones, our genetic studies suggest that the most critical function of PRMT1 is within the centrosome as a regulator of daughter cell counting to assure the proper replication of the parasite.

overall_design: RNA samples were isolated in triplicates from RH-hxgprt parent strain (W), PRMT1 knockout (K) strain and PRMT1 knockout strain complemented with RFP-tagged PRMT1 protein (C). Parasites were grown for 32h at 37C. Samples were hybridized to the Toxoplasma gondii Affymetrix microarray (ToxoGeneChip: http://ancillary.toxodb.org/docs/Array-Tutorial.html). Hybridization data was preprocessed with Robust Multi-array Average (RMA) and normalized using per chip and per gene median polishing and analyzed using the software package GeneSpring GX (Agilent Technologies).

last: S. Suvorova

first: Kami

last: Kim


title: Transcriptome profiling of Lactococcus lactis subsp. cremoris CECT 8666 in response to agmatine

status: Public on Nov 09 2015

city: Villaviciosa

first: Beatriz

last: del Rio

state: Asturias

address: Paseo Rio Linares s/n

department: Technology and Biotechnology of Dairy Products

institute: Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

summary: The goal was to determine the effect of agmatine on the trancriptional profile of L. lactis CECT 8666 strain. For that we compared the expression profile of L. lactis CECT 8666 cells grown in culture medium supplemented with 20 mM agmatine with the expression profile of L. lactis CECT 8666 cells grown in culture medium without agmatine.

platform_organism: Lactococcus cremoris subsp. cremoris GE214

overall_design: L. lactis CECT 8666 cells grown in GalM17 medium (reference) compared to L. lactis CECT 8666 cells grown in GalM17 medium supplemented with 20 mM agmatine (test).

first: Victor

last: Ladero

first: Daniel

middle: M

last: Linares

first: Begoña

last: Redruello

first: Anne

last: de Jong

first: Oscar

middle: P

last: Kuipers

first: Maria

last: Fernandez

first: M

last: Martin

first: Miguel

middle: A

last: Alvarez