title: LncRNAs expression profiles in the livers of C57Bl/6 mice after partial hepatectomy

status: Public on Apr 24 2013

city: Shanghai

first: Dan

last: Xu

address: Xiangyin Road

department: Second Military Medical University

country: China

institute: Mus musculus

summary: Liver regeneration has important implications because many therapeutic strategies for the surgical treatment of liver diseases, such as removal of liver tumors and liver transplantation, depend on the ability of the liver to regenerate physically and functionally. Recent studies reported that lncRNAs control cell proliferation in hepatocellular carcinoma (HCC). However, the role of lncRNAs in liver regeneration and the overall mechanisms remain largely unknown. To address this issue, we carried out a genome-wide lncRNA microarray analysis during liver regeneration in mice after 2/3 partial hepatectomy (PH) at various time points. The results revealed differential expression of thousands of lncRNAs during liver regeneration.

overall_design: Six-week-old male wildtype C57Bl/6 mouse liver samples were obtained at 0, 1.5, 12, and 24 hours after 2/3 PH, and three mice were analyzed for each time point. Total RNA was isolated using Trizol.Mouse Stringent LncRNA Array (4 x 44K, ArrayStar, Rockville, MD) were used to monitor the expression level of approximately 14000 lncRNAs identified from the NCBI RefSeq, UCSC, RNAdb2.0, NRED, Fantom3.0 and UCRs. LncRNAs differentially expressed were identified by comparing expression levels during liver regeneration in mice after 2/3 partial hepatectomy (PH) at various time points.

first: Fu

last: Yang

first: Ji-hang

last: Yuan

first: Ling

last: Zhang

first: Hai-shan

last: Bi

first: Chuan-chuan

last: Zhou

first: Feng

last: Liu

first: Jin-feng

last: Huang

first: Fang

last: Wang

first: Shu-han

last: Sun


title: Gene expression analysis of F9 cells double knock-down for Sox7 and Sox17

status: Public on Apr 23 2013

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

country: France

institute: Stem Cell and Brain Research Institute

summary: Analysis of the expression of F9 cells after knockdown of Sox7 and Sox17 during their primitive endoderm differnetiation induction with retinoic acid. Results provide information on the endodermal gene expression program regulated by Sox7 and Sox17.

overall_design: Sox7 Sox17 double KD vs. control in F9 cells

first: Larry

last: Stanton


title: Fetal mesenchymal stromal cells differentiating towards chondrocytes acquire a gene expression profile resembling human growth plate cartilage.

status: Public on Apr 22 2013

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: We used human fetal bone marrow-derived mesenchymal stromal cells (hfMSCs) differentiating towards chondrocytes as an alternative model for the human growth plate (GP). Our aims were to study gene expression patterns associated with chondrogenic differentiation to assess whether chondrocytes derived from hfMSCs are a suitable model for studying the development and maturation of the GP. hfMSCs efficiently formed hyaline cartilage in a pellet culture in the presence of TGFB3 and BMP6. Microarray and principal component analysis were applied to study gene expression profiles during chondrogenic differentiation. A set of 232 genes was found to correlate with in vitro cartilage formation. Several identified genes are known to be involved in cartilage formation and validate the robustness of the differentiating hfMSC model. KEGG pathway analysis using the 232 genes revealed 9 significant signaling pathways correlated with cartilage formation. To determine the progression of growth plate cartilage formation, we compared the gene expression profile of differentiating hfMSCs with previously established expression profiles of epiphyseal GP cartilage. As differentiation towards chondrocytes proceeds, hfMSCs gradually obtain a gene expression profile resembling epiphyseal GP cartilage. We visualized the differences in gene expression profiles as protein interaction clusters and identified many protein clusters that are activated during the early chondrogenic differentiation of hfMSCs showing the potential of this system to study GP development. To determine the progression of growth plate cartilage formation, we compared the gene expression profile of differentiating hfMSCs with previously established expression profiles of epiphyseal GP cartilage. As differentiation towards chondrocytes proceeds, hfMSCs gradually obtain a gene expression profile resembling epiphyseal GP cartilage. We visualized the differences in gene expression profiles as protein interaction clusters and identified many protein clusters that are activated during the early chondrogenic differentiation of hfMSCs showing the potential of this system to study GP development.

overall_design: RNA fhMSCs of chondrogenically differentiating fhMSCs was isolated at week, 0, 1, 2, 3, 4 and 5. Moreover, RNA of 4 human growth plates from was isolated.

first: Joyce

last: Emons

first: Sandy

last: van Gool

first: Jeroen

middle: C

last: Leijten

first: Marcel

last: Karperien


title: To study gene expression of PHO80-deleted yeast strain in xylose fermentation

city: Kobe

first: Akihiko

last: Kondo

address: 1-1 Rokkodai, Nada

department: Chemical Science and Engineering

country: Japan

institute: Kobe University

summary: The main objective is to improve xylose fermentation by deletion of PHO80 gene in recombinant xylose-fermenting yeast strains. Microarray analysis was performed to investigate effects of PHO80 deletion on the gene expression profile of xylose-fermenting strains.

overall_design: Samples for 2 strains (wild-type control, PHO80-deleted strain) were taken after 6h of xylose fermentation. Each sample was triplicated, resulting in a total of 6 samples.

first: Keisuke

last: Fujitomi

first: Tomohisa

last: Hasunuma


title: Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum G186AR

status: Public on Apr 10 2013

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

country: USA

institute: University of California

summary:
Histoplasma capsulatum is a fungal pathogen that infects both healthy and immunocompromised hosts. In endemic regions, H. capsulatum grows in the soil and causes respiratory and systemic disease when inhaled by humans. An interesting aspect of H. capsulatum biology is that it adopts specialized developmental programs in response to its environment. In the soil, it grows as filamentous chains of cells (mycelia) that produce asexual spores (conidia). When the soil is disrupted, conidia aerosolize and are inhaled by mammalian hosts. Inside a host, conidia germinate into yeast-form cells that colonize immune cells and cause disease. Despite the ability of conidia to initiate infection and disease, they have not been explored on a molecular level. Here we develop methods to purify H. capsulatum conidia and show that these cells germinate into either filaments at room temperature or into yeast-form cells at 37C. Conidia internalized by macrophages germinate into the yeast form and proliferate within the macrophages, ultimately lysing the host cells. Similarly, infection of mice with purified conidia is sufficient to establish infection and yield viable yeast-form cells in vivo. To characterize conidia on a molecular level, we perform whole-genome expression profiling of conidia, yeast, and mycelia from two highly diverged H. capsulatum strains. In parallel, we use homology and protein domain analysis to manually annotate the predicted genes of both strains. Analyses of the resultant data define sets of transcripts that reflect the unique molecular states of H. capsulatum conidia, yeast and mycelia.

This series gives the results for the G186AR strain.

overall_design: Samples were labeled with Cy5 or with Cy3 and competitively hybridized to custom glass slide 70-mer oligomer microarrays in a closed-circuit experimental design (e.g. direct, pairwise comparisons of yeast and mycelial samples, mycelial and conidial samples, and yeast and conidial samples). Dye-swap hybridizations were performed for these pairwise comparisons, as well as an additional technical replicate hybridization for the conidia/yeast comparison, for a total of 7 hybridizations.

first: Diane

middle: O

last: Inglis

first: Anita

last: Sil


title: Identification of nine genomic regions of amplification in bladder cancer, correlation with stage, and potential prognositic and therapeutic value

status: Public on Apr 29 2013

city: Boston

first: Markus

last: Riester

state: MA

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

summary: We sought to test the hypothesis that ascertainment of genome-wide copy number alterations in bladder cancer may have value for clinical management. We performed a genome wide analysis of 164 bladder cancer samples and 27 bladder cancer cell lines to identify genetic changes associated with disease characteristics. Multiplex inversion probe (MIP) analysis, a newly developed genomic technique, was used to study 80 bladder cancers to identify mutations and copy number changes. Selected amplification events were then analyzed in a validation cohort of 84 bladder cancers by multiplex ligation-dependent probe assay (MLPA). In the MIP analysis, 44 regions of significant copy number change were identified using GISTIC. Nine gene-containing regions of amplification were selected for validation in the second cohort by MLPA. Amplification events at these 9 genomic regions were found to correlate strongly with stage, being seen in only 2 of 23 (9%) Ta grade 1 or 1-2 cancers, in contrast to 31 of 61 (51%) Ta grade 3 and T2 grade 2 cancers, p < 0.001. These observations suggest that analysis of genomic amplification of these 9 regions might serve as a guide for clinical decision making, in terms of management decisions following transurethral resection of bladder cancers. This approach is facilitated by the capability of each of the MIP and MLPA methods to analyze formalin-fixed paraffin-embedded DNA, as done here. Furthermore several of the amplified genes identified here (ERBB2, MDM2, CCND1) render the bladder cancers potentially sensitive to targeted therapy.

overall_design: Copy number profiling was completed for 80 urothelial carcinoma samples using the Affymetrix OncoScan(TM) FFPE Express platform.


title: Murine polyploid trophoblast giant cells (TGCs) from day E9.5 implantation sites (experimental) vs E9.5 diploid embryos (control)

status: Public on Apr 30 2013

city: Cambridge

first: Jessica

last: Von Stetina

address: 9 Cambridge Center

institute: Whitehead Institute

type: Genome variation profiling by genome tiling array

summary: Array-based quantitative genome hybridization (aCGH) was performed to quantify gene copy number across the euchromatic portion of the genome of polyploid TGCs relative to embryonic diploid control cells.

overall_design: DNA was prepared from diploid embryonic cells and purified polyploid TGCs, labeled, and hybridized to microarrays. Experiment was performed in two biological replicates.

first: Noa

last: Sher

middle: R

first: George

middle: W

last: Bell

first: Shinobu

last: Matsuura

first: Katya

last: Ravid

first: Terry

middle: L

last: Orr-Weaver


title: Differential gene expression by NKX2-1 suppression in NCI-H2009 cells

status: Public on Apr 15 2013

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: The NKX2-1 transcription factor, a regulator of normal lung development, is the most significantly amplified gene in human lung adenocarcinoma. To better understand how genomic alterations of NKX2-1 drive tumorigenesis, we generated an expression signature associated with NKX2-1 amplification in human lung adenocarcinoma, and analyzed DNA binding sites of NKX2-1 by genome-wide chromatin immunoprecipitation from NKX2-1-amplified human lung adenocarcinoma cell lines.  Combining these expression and cistromic analyses identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1, in addition to consensus binding motifs including a nuclear hormone receptor signature and a Forkhead box motif in NKX2-1-bound sequences.  RNA interference analysis of NKX2-1-amplified cells compared to non-amplified cells demonstrated that LMO3 mediates cell proliferation downstream of NKX2-1; cistromic analysis that NKX2-1 may cooperate with FOXA1.  Our findings provide new insight into the transcriptional regulatory network of NKX2-1 and suggest that LMO3 is a transducer of lineage specific cell survival of NKX2-1-amplified lung adenocarcinomas.

overall_design: NCI-H2009 cells with stable expression of either pLKO-Tet-Op-shGFP (n=4) or pLKO-Tet-Op-shNKX2-1 (pooled population; n=3 and a clone; n=3) were treated with 50ng/ml of doxycyline for 48 hours. Total RNA was extracted, gene expression profiling was performed and differential gene expression between shGFP and shNKX2-1 was analyzed to determine the effects by suppression of NKX2-1 in NCI-H2009 cells.


title: Transcriptome analysis of Enterococcus faecalis OG1 delta-EF2638 mutant

city: Milwaukee

first: Dusanka

last: Vesic

state: Wisconsin

address: 8701 Watertown Plank Road

department: Microbiology and Molecular Genetics

institute: Medical College of Wisconsin

summary:
Analysis of changes in gene expression in Enterococcus faecalis OG1 delta-EF2638 mutant compared to wild-type OG1 strain. The deletion mutant has a growth defect when grown with aeration
The mutant presented in this study is described and characterized in Vesic, D. and Kristich, C.J. 2012. A Rex-family transcriptional repressor influnces H2O2 accumulation by Enterococcus faecalis. (submitted for publication)

overall_design: Microarray analysis was done using RNA isolated from two independent cultures of wild-type Enterococcus faecalis OG1 and two independent cultres of Enterococcus faecalis OG1 delta-EF2638 mutant; each RNA sample was subjected to triplicate hybridization (technical replicates) . Microarrays were custom designed to investigate expression of ORFs in Enterococcus faecalis OG1RF genome. The arrays were designed based on the OG1RF annotation generated with the Rapid Annotation Using Subsystem Technology (RAST) server (Aziz et. al. 2008. BMC Genomics 9:75), as described in Frank et al (2012) Infect. Immun. 80:539.  The aim was eighteen probe pairs per ORF, each of which is present in triplicate.

first: Chris

last: Kristich


title: Bmi1 mutant vs. WT dental epithelia

status: Public on Apr 12 2013

first: Brian

last: Biehs

address: 505 Parnassus Ave

institute: UCSF

summary: Transcriptional profiling of Bmi1 mutant dental epithelia including the stem cell compartment to determine which genes are upregulated in response to loss of Bmi1.

overall_design: Two condition experiment: dental epithelia homozygous null for Bmi1 and WT dental epithelia. 4 replicates each


title: Identification of an effective early signaling signature during neo-vasculogenesis in vivo by ex vivo proteomic profiling

status: Public on Apr 09 2013

city: Graz

first: Rokhsareh

last: Rohban

address: Stiftingtalstrasse 24

country: Austria

institute: Medical University Graz

summary: Therapeutic neo-vasculogenesis in vivo can be achieved by the co-transplantation of human endothelial colony-forming progenitor cells (ECFCs) with mesenchymal stem/progenitor cells (MSPCs).The underlying mechanism is not completely understood thus hampering the development of novel stem cell therapies.We hypothesized that proteomic profiling could be used to retrieve the in vivo signaling signature during the initial phase of human neo-vasculogenesis. ECFCs and MSPCs were therefore either transplanted alone or co-transplanted subcutaneously into immune deficient mice. Early cell signaling, occurring within the first 24 hours in vivo, was analyzed using antibody microarray proteomic profiling.Vessel formation and persistence were verified in parallel transplants for up to 24 weeks.   Proteomic analysis revealed significant alteration of regulatory components including caspases, calcium/calmodulin-dependent protein kinase, DNA protein kinase,human ErbB2 receptor-tyrosine kinase as well as mitogen-activated protein kinases.Therapeutic candidate caspase-4 was selected from array results for targeting vascular network formation in vitro as well as modulating therapeutic vasculogenesis in vivo. As a proof-of-principle, caspase-4 and general caspase-blocking led to diminished endothelial network formation in vitro and significantly decreased vasculogenesis in vivo. Proteomic profiling ex vivo thus unraveled a signaling signature which can be targeted to modulate neo-vasculogenesis in vivo.

overall_design: A number of four microarrays (with two fields on each array) were used with the possibility to load and analyze two samples side by side at the same time.Therefore, a total number of eight samples were loaded and analyzed in this study. All microarrays contained the pooled protein content (N=3) of MSPC+ECFC in vivo plugs in one field and the other field was filled with the pooled protein extraction (N=3) of MSPC only plugs in vivo (Array#1), pooled protein extraction (N=3) of ECFC only plugs in vivo (Array#2),  cell-free Matrix (Matrigel, Milipore) as the control (Array#3) and pooled protein extraction (N=3) of the MSPC+ECFC plugs in vitro (Array#4). Arrays#1,2 and 4 were used as reference samples and cell-free Matrix (Array#3) was used as the control.

first: Nathalie

last: Etchart

first: Andreas

last: Reinisch

first: Eva

last: Rohde

first: Dirk

last: Strunk


title: Expression analysis of prostate tissue on locus 8q24

status: Public on Apr 11 2013

city: Reykjavik

first: Sigrun

middle: Helga

last: Lund

address: Dunhagi 3

country: Iceland

institute: University of Iceland

type: Expression profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Serum miRNA profiles of patients with oral cancer and pre-cancer

city: Vancouver

first: Sara

last: MacLellan

state: British Columbia

address: 675 West 10 Ave

country: Canada

institute: BC Cancer Research Centre

summary: The aim of this study was to examine the expression profiles of circulating miRNAs in the serum of patients with high-risk oral lesions (HRLs; oral cancer or carcinoma in situ) and to explore their utility as potential oral cancer biomarkers. Global serum miRNA profiles were generated by quantitative PCR method from 1) patients diagnosed with HRLs and undergoing intent-to-cure surgical treatment (N = 30) and 2) a demographically-matched, normal control group (N = 26). We next honed our list of serum miRNAs associated with disease by reducing the effects of inter-patient variability; we compared serum miRNA profiles from samples taken both before and after tumor resections (N = 10). Based on these analyses, fifteen miRNAs were significantly up-regulated and five were significantly down-regulated based on presence of disease (minimum fold-change >2 in at least 50% of samples, p < 0.05, permutation t-test). Five of these miRNAs (miR-16, let-7b, miR-338-3p, miR-223, and miR-29a) yielded an area under the ROC curve (AUC) >0.8, suggesting utility as non-invasive biomarkers for detection of oral cancer or high grade lesions.

overall_design:
qPCR miRNA expression profiling of serum samples. The sample size for control and HRL cases are indicated in the summary. The samples were not processed in replicate.
Dataset 1: Samples from pre-surgery HRL patients (N = 30) and normal controls (N = 26).
Dataset 2: Samples taken both before and after tumor resections (N = 10). Processed separately from Dataset 1.

middle: A

first: Cathie

last: Garnis

first: Catherine

middle: F

last: Poh


title: Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum

first: Mark

last: Voorhies


title: Gene expression in CF-vs-non CF human airway epithelial cell samples obtained by nasal brushing.

city: Lisboa

first: Luka

last: Clarke

address: Campo Grande

department: BioFIG

country: Portugal

institute: University of Lisboa

summary:
A small-scale whole genome microarray study of gene expression in human native nasal epithelial cells from F508del-CFTR homozygous CF patients and non-CF controls.
We used the custom designed Affymetrix HsAirwaya520108F Arrays to compare gene expression in 5 CF and 5 non CF nasal epithelial cell samples.

overall_design: We analysed a total of 10 samples (5 CF and 5 non CF). The CF group contained 2 males and 3 females, with an average age of 14 years and an average of 6% inflammatory cells per sample, and the non CF group  contained 3 males and 2 females with an average age of 14.8 years and an average of 4.7% inflammatory cells.

first: Lisete

last: Sousa

first: Margarida

middle: D

last: Amaral


title: Linalool, an aromatic terpenoid, rewires transcriptome profile of lipid-loaded HepG2 cells

city: Seoul

first: Sung-Joon

last: Lee

address: 402, Bioth Building (east) Anam 5 ga, Seungbuk gu

country: South Korea

institute: Korea University

summary: The microarray results showed that linalool sitimulation of lipid-loaded HepG2 cells rewired the hepatic transcriptome profile, with linalool being comparable to those of fenofibrate. Total of 8,988 genes that were commonly and significantly expressed in all experimental groups, including control hepatocytes, lipid-loaded hepatocytes, and lipid-loaded hepatocyted stimulated with linalool or fenofibrate, respectively, to compare the transcriptome profile of linalool (1mM) with those of hypotriglyceridemic drug, fenofibrate (100 μM). Lipid loading of hepatocytes notably changed hepatic transcriptome profile, where 77 % of the selected genes showed >20% changes in expression (fold change > 1.2 or fold change <0.8). However, linalool stimulation of lipid-loaded cells showed that 48 % of the selected genes had expression changes of >20%. Thus, 29 % of the selected genes became to show less than 20% changes in expression after linalool stimulation compared to the lipid-loaded condition. Fenofibrate showed 46 % of the selected gene expression changes of >20%. Thus, 31 % of the seleted genes fell into the <20% change category compared to the lipid-loaded condition after fenofibrate stimulation.

overall_design: Untreated control vs. lipid-loaded HepG2 cells (3 biological replicates), untreated control vs. lipid-loaded HepG2 cells treated with fenofibrate (3 biological replicates), untreated control vs. lipid-loaded HepG2 cells treated with linalool (2 biological replicates). One replicate per array

first: Hee-Jin

last: Jun

first: Jinyoung

last: Kim

first: Yaoyao

last: Jia

first: Minh-Hien

last: Hoang

first: Kyoung-Heon

first: Eun-Ju

last: Yun

first: Kwang-Yeon

last: Hwang


title: Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum G217B

summary:
Histoplasma capsulatum is a fungal pathogen that infects both healthy and immunocompromised hosts. In endemic regions, H. capsulatum grows in the soil and causes respiratory and systemic disease when inhaled by humans. An interesting aspect of H. capsulatum biology is that it adopts specialized developmental programs in response to its environment. In the soil, it grows as filamentous chains of cells (mycelia) that produce asexual spores (conidia). When the soil is disrupted, conidia aerosolize and are inhaled by mammalian hosts. Inside a host, conidia germinate into yeast-form cells that colonize immune cells and cause disease. Despite the ability of conidia to initiate infection and disease, they have not been explored on a molecular level. Here we develop methods to purify H. capsulatum conidia and show that these cells germinate into either filaments at room temperature or into yeast-form cells at 37C. Conidia internalized by macrophages germinate into the yeast form and proliferate within the macrophages, ultimately lysing the host cells. Similarly, infection of mice with purified conidia is sufficient to establish infection and yield viable yeast-form cells in vivo. To characterize conidia on a molecular level, we perform whole-genome expression profiling of conidia, yeast, and mycelia from two highly diverged H. capsulatum strains. In parallel, we use homology and protein domain analysis to manually annotate the predicted genes of both strains. Analyses of the resultant data define sets of transcripts that reflect the unique molecular states of H. capsulatum conidia, yeast and mycelia.

This series gives the results for the G217B strain.

overall_design: Samples were labeled with Cy5 or with Cy3 and competitively hybridized to custom glass slide 70-mer oligomer microarrays in a closed-circuit experimental design (e.g. direct, pairwise comparisons of yeast and mycelial samples, mycelial and conidial samples, and yeast and conidial samples). Dye-swap hybridizations were performed for these pairwise comparisons, and hybridizations to an additional conidial biological replicate were performed for the conidia/yeast and conidia/mycelia comparisons, for a total of 8 hybridizations.

first: Diane

last: Inglis

first: Anita

last: Sil


title: Real-time PCR analysis of microRNA expression in differentiating human skeletal muscle cells

city: Gif Sur Yvette Cedex

first: Guillaume

last: PINNA

address: Bat. 144 - Point courrier n° 22 - CEA SACLAY

institute: CEA

summary:
Human skeletal myoblast cell line LHCN-M2 (Zhu et al., Aging Cell (2007), vol. 6, pp 515-523) were plated on collagen-coated 6-well Falcon cell culture plates at 500 000 cells/well, differentiation was induced 24h later by switching to DMEM supplemented with 0,01 mg/ml insulin and 0,1 mg/ml transferrin. Cells were collected at 0, 3, and 7 days of differentiation time points.
Total RNA was extracted and miRNA expression evaluated by quantitative real-time PCR.

overall_design: MiRNA expression profiling in proliferating and differentiating (3 and 7 days) human skeletal myoblasts LHCN-M2.

first: Anna

last: Polesskaya

last: Pinna


title: Autoantibodies are abundant in all human sera: a demographic characterization via protein microarrays

status: Public on Apr 25 2013

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

summary: Human serum samples were probed onto human protein microarrays in order to ascertain the number and diversity of naturally ocurring self-reactive IgG autoantibodies.

overall_design: In the study presented here, 166 human serum samples were probed onto human protein microarrays in order to identify self-reactive IgG autoantibodies and study their number and diversity in variable donor demographics.  Microarray data were analyzed using several statistical programs, including Prospector v5.2, and autoantibodies with a relative fluorescence Z-factor value of greater than or equal to 0.4 were considered significant.

first: Eric

middle: P

first: Min

last: Han

first: Cassandra

last: DeMarshall

first: Nimish

last: Acharya


title: Expression analysis of prostate tissue on locus 8q24 part 2

first: Sigrun

last: Lund

summary:
Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24.
The region chr8:127640000-129120000 is tiled with isothermal probes (hg17)

overall_design: 7 chip study, using 7 independent samples.

middle: H


status: Public on Apr 05 2013

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary: Transcriptional profiles on different yeast strain mutants (DEgd2/1, DEgd2/Btt1)were identified by microarray analysis comparing total mutant RNA vs wild type RNA.

overall_design: Set of arrays that are part of repeated experiments

first: Marta

last: Del Alamo


title: Pyrosequencing Analysis of Microbial Communities in Rock Varnish

status: Public on Apr 26 2013

city: Madison

first: Andrew

last: Corcoran

address: 1415 Engineering Drive

department: Civil and Environmental

institute: UW-Madison

summary: This study investigated the microbial community of rock varnish

overall_design: Based on consensus sequences for 16S OTUs

first: Kimberly

last: Kuhlman

first: Daniel

last: Noguera


title: Single case sample of a Non-Hodgkin lymphoma

status: Public on Apr 13 2013

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

summary: Our study provides evidence that JAK2, PDL1 and PDL2 are recurrently affected by structural and numerical aberrations in lymphoid neoplasms. The study highlights the role of PDL1/PDL2 in lymphoma progression.

overall_design: single case analysis

first: Katrien

last: Van Roosbroeck

last: Ferreiro

first: Thomas

last: Tousseyn

first: Jo-Anne

last: van der Krogt

first: Lucienne

last: Michaux

first: Iwona

last: Wlodarska


title: Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes.

type:
Expression profiling by array
Other


title: Characterization of the lag-phase associated cold acclimation gene expression responses in L. monocytogenes EGD-e

status: Public on Apr 19 2013

city: Zurich

first: Carolina

last: Arguedas-Villa

state: Zurich

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

summary: Gene expression changes in L. monocytogenes EGDe during lag-phase associated cold acclimation were succesfully defined through expression profiling

overall_design: The gene expression profiles of L. monocytogenes EGD-e cells that underwent cold acclimation during lag phase were analyzed in a genome-wide microarray assay with a total of 2847 genes, were the resulting significantly regulated genes were splitted in two groups (up-and down-regulated)

first: Taurai

last: Tasara

first: Roger

last: Stephan


title: Polysomes

summary: Translational profiles of wild type yeast strains were identified by microarray analysis by isolating polysomes using sucrose gradients to recover polysome-associated RNA and comparing polysome-associated RNA vs total RNA

last: Hogan


title: Expression analysis of prostate tissue on locus 8q24 part 3

last: Lund

summary: Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24.

overall_design: 3 chips with 3 arrays each study, using 3 pairs of normal vs. tumor tissue and 3 replicates of the same sample. Each chip contained one pair of normal vs. tumor and one copy of the repeated sample.


title: Expression analysis of prostate tissue on locus 8q24 part 1

summary:
Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24.
The region chr8:127640000-129120000 is tiled with 60 nt probes at 10 nt interval (hg18)


title: TGF-beta 1 effect on primary bovine aortic endothelial cells

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Analysis of primary bovine aortic endothelial cells treated for 24 hours with TGF-beta 1 5 ng/ml. TGF-beta 1 has been shown to induce endothelial-to-mesenchymal transition (EndoMT) and to be implicated in differentiation of endothelial cells into smooth muscle-like cells as occurred in vascular neointimal formation.

overall_design: Primary aortic endothelial cells seeded on 10 mm diameter plates were incubated with TGF-beta 1 (5 ng/ml) for 24 hours or left under basal conditions. Triplicates from three different cultures.

first: Oscar

last: Busnadiego

first: David

last: Lagares

first: Fernando

last: Rodríguez-Pascual


title: 24-hour herbivory exposure of VHb-expressing Populus tremula x Populus tremuloides

city: Oulu

first: Suvi

middle: Tuulia

last: Sutela

department: Biology

country: Finland

institute: University of Oulu

summary: The expression of stress-related genes induced by feeding of chestnut moth larvae (Conistra vaccinii L.) was studied with Vitreoscilla hemoglobin-expressing (VHb) and non-transgenic hybrid aspen lines (Populus tremula x P. tremuloides). Besides the herbivore-injured leaves (L1), cDNA microarray analyses were conducted using uninjured leaves of hybrid aspen lines positioned above (A) and below (B) the herbivory exposed leaves.

overall_design:
Two-condition experiment, control vs. herbivory exposure. Two hybrid aspen lines: non-transgenic V617 and VHb expressing V617 /45. Of each plant, three leaf types were analysed: the injured/uninjured leaf (L1) and nonorthostichous leaf positioned above (A) and below (B).
Biological replicates: 3. On each array, two samples representing L1, A or B leaf type of control and herbivory treatment of either V617 or V617/45 line.

line V617: wt_A_rep1-3, wt_B_rep1-3, wt_L1_rep1-3
line V617/45: VHb_A_rep1-3, VHb_B_rep1-3, VHb_L1_rep1-3
leaf type A: wt_A_rep1-3, VHb_A_rep1-3
leaf type B: wt_B_rep1-3, VHb_B_rep1-4
leaf type L1: wt_L1_rep1-3, VHb_L1_rep1-5

first: Soile

last: Jokipii-Lukkari

first: Anna

middle: K

last: Anttila

first: Tiina

last: Ylioja

first: Hely

last: Häggman


title: RNA coimmunoprecipitations

last: Stanford Microarray Database

summary: Nascent polypeptides emerging from the ribosome during biogenesis can interact with many chaperones and protein homeostasis factors. The high sensitivity of RNA identification can be used to identify substrates of specific cotranslationally acting chaperones. Protein A-tagged (TAP-tag) chaperones associated with translating ribosomes were immunopurified by binding to magnetic IgG beads, washed, and chaperone complexes were eluted with TEV protease treatment. Immunopurified RNAs and total cell extract RNAs were isolated, reverse transcribed, coupled to Cy5 and Cy3 dyes, respectively, and comparatively hybridized to DNA microarrays

first: Daniel

first: Marta

last: Del Alamo


title: RNA messengers translated at the ER membrane

summary: In order to identify what RNA messengers are being translated at the ER membrane, membrane-associated polysomes were separated from free polysomes by subcellular fractionation of WT and delta-egd1/delta-egd2 yeast strains and associated RNA was isolated and then identified by microarray analysis.


title: RNA sampling from a chemically diverse set of solid agar cultures of Aspergillus nidulans

status: Public on Apr 04 2013

city: Kgs. Lyngby

first: Mikael

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

summary: In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 out of 16 known clusters and nearly accurate for the remaining three. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (super clusters), and validate this both with legacy data and experimentally by prediction and verification of a new supercluster consisting of the synthase AN1242 and the transferase AN11080. This normally requires extensive sets of combinatorial gene deletions. We have employed A. nidulansfor our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom.

overall_design: RNA was sampled from stabbed cultures on three different solid agar-based media (CYAs, YES, CYA) after 4, 8 or 10 days, resulting in a total of 8 samples.

first: Mia

last: Zachariasen

first: Lene

last: Blicher

first: Kristian

last: Nielsen

first: Uffe

last: Mortensen


title: NO001: Kdm5c controls promoter and enhancer activities

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: The functional organization of eukaryotic genomes correlates with specific patterns of histone methylations. Regulatory regions in genomes like enhancers and promoters differ in their extent of methylation of histone H3 at lysine-4 (H3K4), but it is largely unknown how the different methylation states are specified and controlled. Here, we show that the Kdm5c/Jarid1c/SMCX member of the Kdm5 family of H3K4 demethylases can be recruited to both enhancer and promoter elements in embryonic stem cells and neuronal progenitor cells via gene-specific transcription factors. Knockdown of Kdm5c deregulates transcription via local increases in H3K4me3. Our data show that restricting H3K4me3 modification at core promoters dampens transcription, but Kdm5c is required at enhancers for their full activity. Remarkably, an impaired enhancer function activates the intrinsic promoter activity of Kdm5c-bound distal elements. Our results demonstrate that the Kdm5c demethylase plays a crucial and dynamic role in the functional discrimination between enhancers and core promoters.

overall_design: RNA from four independent cultures from each sh Kdm5c #1, sh Kdm5c #2 and non-targeting shRNA polyclonal cell lines were hybridized in dye-swap against a common reference of RNA from IB10 ES cells.

first: Nikolay

middle: S

last: Outchkourov

first: Jose

middle: M

last: Muino

first: Kerstin

last: Kaufmann

first: Wilfred

last: van IJcken

middle: J

first: Dik

last: van Leenen

first: Frank

last: Holstege

last: Grosveld

first: H

last: Timmers


title: Gene expression and pathologic alteration in juvenile rainbow trout due to chronic dietary TCDD exposure

city: St John's

first: Tiago

last: Hori

state: NL

address: 0 Marine Lab Rd

department: Ocean Sciences Centre

institute: Memorial University of Newfoundland

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

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design: Refer to individual Series


title: Determination of the serum miRNA expression profile in human moyamoya disease (MMD)

city: Shanghai

first: Dongwei

last: Dai

address: 168 Changhai Road

institute: Changhai Hospital

summary: Moyamoya disease (MMD) is a cerebrovascular disease characterized by progressive stenosis of the intracranial internal carotid arteries and their proximal branches. However, the etiology of this rare disease remains widely unknown. Serum microRNA (miRNA) profiles have been screened to identify novel biomarkers for disease diagnosis and prognosis. Here, we identified important serum miRNAs that might play important roles in contributing to MMD pathogenesis through microarray analysis.

overall_design: 10 MMD patients and 10 controls were consecutively recruited at Shanghai Changhai Hospital. Five-ml venous blood was collected from each participant and separated into serum and cellular fractions. We pooled serum samples from 10 MMD patients and 10 controls. Agilent Human 8 x 60K miRNA Array was performed on the two pooled samples.


title: Dose-dependent effects of TCDD in juvenile rainbow trout

summary: We investigated the effects of chronic TCDD exposure on global gene expression in developing rainbow trout (Oncorhynchus mykiss). Juvenile rainbow trout (0.18±0.01g) were fed Biodiet starter with TCDD added at 0, 0.1, 1, 10 and 100ppb, and ten fish were sampled and pooled from each group for microarray experiments at 28 days after initiation of the exposure. Gene expression analysis was performed using the Genomics Research on All Salmonids Project (cGRASP) 16K cDNA microarrays. TCDD-responsive whole body transcripts identified in the microarray experiments have putative functions involved in various biological processes including cellular process, metabolic process, biological regulation, and response to stimulus. In addition, TCDD caused leisons in multiple organ systems in juvenile rainbow, including skin, oropharynx, liver, gas bladder, intestine, pancreas, nose and kidney.

overall_design: Juvenile rainbow trout (0.18±0.01g) were fed Biodiet starter (Bio-Oregon) (4% body weight per day) with TCDD added at 0, 0.1, 1, 10 and 100 ppb. Fish were sampled after 28 days. Total RNA from individual fish was isolated using TRIzol reagent (Invitrogen). Total RNA of ten control trout were pooled as a common reference which were labeled with Cy3. Total RNA of ten fish of each treatment were labeled wih Cy5. cDNA were synthesized using SuperScript II Reverse Transcriptase (Invitrogen) (1 μg pooled RNA per synthesis). Targets were labeled using the Array 900 Expression Array Detection kit (Genisphere) following the manufacture protocol. 1µg RNA of pooled ten control fish were labled with Cy3 and 1µg RNA of pooled ten TCDD-treated fish were labled with Cy5, then day-swap was performed. Two arrays were run for each comparison. Microarrays were scanned at 10 µm resolution using a ScanArray Express (PerkinElmer Life Sciences, Inc, Boston, MA). The photomultiplier tube settings (PMT) for Cy3 and Cy5 were 70 and 65-66, respectively. TIFF images of arrays were generated with ScanArray Express software (PerkinElmer). Fluorescence intensity data for Cy3 and Cy5 channels were extracted from TIFF images using ImaGene 7.5 software (BioDiscovery Inc., El Segundo, CA). Background correction, data transformation (setting background corrected values < 0.01 to 0.01), Lowess normalization, and analysis (e.g. fold-change calculations) were performed using GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA)

first: Qing

last: Liu

first: Matthew

last: Rise

first: Michael

last: Carvan


title: Time-dependent toxic effects of dietary TCDD in juvenile rainbow trout

summary: We investigated the effects of chronic TCDD exposure on global gene expression in developing rainbow trout (Oncorhynchus mykiss). Juvenile rainbow trout(0.18±0.01g) were fed Biodiet starter with TCDD added at 0, 0.1, 1, 10 and 100ppb, and ten fish were sampled and pooled from 10 ppb group at 7, 14, 28 and 42 days for microarray experiments after initiation of the exposure. Gene expression analysis was performed using the Genomics Research on All Salmonids Project (cGRASP) 16K cDNA microarrays. TCDD-responsive whole body transcripts identified in the microarray experiments have putative functions involved in various biological processes including response to stimulus, cell wall organization or biogenesis, growth and cell proliferation. In addition, TCDD caused leisons in multiple organ systems in juvenile rainbow, including skin, oropharynx, liver, gas bladder, intestine, pancreas, nose and kidney.

overall_design: Juvenile rainbow trout (0.18±0.01g) were fed Biodiet starter (Bio-Oregon) (4% body weight per day) with TCDD added at 0, 0.1, 1, 10 and 100 ppb. Fish were sampled and from 10 ppb group at 7, 14, 28 and 42 days for microarray experiments after initiation of the exposure. Total RNA from individual fish was isolated using TRIzol reagent (Invitrogen).Total RNA of ten control trout were pooled as a common reference which were labeled with Cy3. Total RNA of ten fish of each treatment were labeled wih Cy5. cDNA were synthesized using SuperScript II Reverse Transcriptase (Invitrogen) (1 μg pooled RNA per synthesis). Targets were labeled using the Array 900 Expression Array Detection kit (Genisphere) following the manufacture protocol. 1µg RNA of pooled ten control fish were labled with Cy3 and 1µg RNA of pooled ten TCDD-treated fish were labled with Cy5, then day-swap was performed. Two arrays were run for each comparison. Microarrays were scanned at 10 µm resolution using a ScanArray Express (PerkinElmer Life Sciences, Inc, Boston, MA). The photomultiplier tube settings (PMT) for Cy3 and Cy5 were 70 and 65-66, respectively. TIFF images of arrays were generated with ScanArray Express software (PerkinElmer). Fluorescence intensity data for Cy3 and Cy5 channels were extracted from TIFF images using ImaGene 7.5 software (BioDiscovery Inc., El Segundo, CA). Background correction, data transformation (setting background corrected values < 0.01 to 0.01), Lowess normalization, and analysis (e.g. fold-change calculations) were performed using GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA)


title: Linalool-responsive genes in linalool synthase-overexpressing transgenic rice

status: Public on Apr 01 2013

city: miki

first: kenji

last: gomi

state: kagawa

institute: Kagawa University

summary: The plant volatile linalool plays important roles in the regulation of defense responses in rice. To clarify the response to linalool in rice at gene expression level, we performed a microarray analysis using the Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA). As a result, many defense-related genes including pathogenesis-related (PR) genes were upregulated in the linalool synthase-overexpressing transgenic rice.

overall_design: An Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA) was used for the microarray analysis. Total RNA was extracted from leaf blades of four-leaf stage rice plants. Line 13 was used as the linalool synthase-overexpressing transgenic rice plant. For each biological replicate, material from at least three rice plants was pooled to provide a single sample for RNA extraction. We performed 3 biological replicates for each treatment. All microarray procedures and data analyses were performed according to the manufacturer’s instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (100 ng) was labeled with Cy-3 using an Agilent Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65°C. After hybridization, following wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2565CA; Agilent Technologies). Feature extraction software (Agilent Feature Extraction; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.

first: Kenji

last: Gomi

first: Shiduku

last: Taniguchi

first: Yumi

last: Hosokawa-Shinonaga

first: Kazuya

last: Akimitsu


title: The stringent response of Staphylococcus aureus and its impact on survival after phagocytosis through the induction of intracellular PSMs expression

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary: The stringent response is initiated by rapid (p)ppGpp synthesis, which leads to a profound reprogramming of gene expression in most bacteria. The stringent phenotype seems to be species specific and may be mediated by fundamentally different molecular mechanisms. In Staphylococcus aureus, (p)ppGpp synthesis upon amino acid deprivation is achieved through the synthase domain of the bifunctional enzyme RSH (RelA/SpoT homolog). In several firmicutes, a direct link between stringent response and the CodY regulon was proposed. Wild-type strain HG001, rshSyn, codY and rshSyn, codY double mutants were analyzed by transcriptome analysis to delineate different consequences of RSH-dependent (p)ppGpp synthesis after induction of the stringent response by amino-acid deprivation. Under these conditions genes coding for major components of the protein synthesis machinery and nucleotide metabolism were down-regulated only in rsh positive strains. Genes which became activated upon (p)ppGpp induction are mostly regulated indirectly via de-repression of the GTP-responsive repressor CodY. Only seven genes, including those coding for the cytotoxic phenol-soluble modulins (PSMs), were found to be up-regulated via RSH independently of CodY. qtRT-PCR analyses of hallmark genes of the stringent response indicate that an RSH activating stringent condition is induced after uptake of S. aureus in human polymorphonuclear neutrophils (PMNs). The RSH activity in turn is crucial for intracellular expression of psms. Accordingly, rshSyn and rshSyn, codY mutants were less able to survive after phagocytosis similar to psm mutants. Intraphagosomal induction of psma1-4 and/or psmß1,2 could complement the survival of the rshSyn mutant. Thus, an active RSH synthase is required for intracellular psm expression which contributes to survival after phagocytosis.

overall_design: Microarray was used to evaluate alteration in the transcriptome of codY and rsh mutants and compared to the wild type

first: Tobias

last: Geiger

first: Patrice

last: Francois

first: Manuel

last: Liebeke

first: Martin

last: Fraunholz

first: Christiane

last: Goerke

first: Bernhard

last: Krismer

first: Jacques

last: Schrenzel

last: Lalk

last: Wolz


title: A whole-blood RNA transcript based prognostic model in castration-resistant prostate cancer

status: Public on Apr 02 2013

city: New York

last: Galsky

address: 1 Gustave L Levy Place

institute: Mount Sinai School of Medicine

summary: Peripheral blood from 62 men with castration resistant prostate cancer was collected between 8/2006 and 6/2008. A panel of 168 inflammation-related and prostate cancer related genes was assessed with quantitative PCR to assess biomarkers predictive of survival.

overall_design: qPCR profiling of whole blood from patients with castration-resistant prostate cancer.

first: M

first: W

last: Oh


title: Molecular Characterization of the Vasculature of Patients with Infiltrating Ductal Carcinoma generates a Gene Signature predictive of Breast Cancer Survival

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

summary: Introduction: Targeting of the tumor vasculature has evolved into an integral part of existing standard anti-cancer therapies. However, recent pre-clinical and clinical studies have shown that the efficacy of these treatments is temporary at most and frequently followed by the renewed tumor growth, indicating that these targets may not be robust.   Methods: We transcriptionally profiled laser capture microdissection isolated microvessels from tumor and matching adjacent normal tissue samples obtained from breast cancer patients diagnosed with infiltrating ductal carcinoma. Gene expression profiles were generated and analyzed using Genespring and the web-based WebGestalt bioinformatics Toolkit. Several differentially expressed genes were validated by immunohistochemistry. To further mine our data set we used a novel integrative systems biology network approach to identify a gene signature that could robustly stratify breast cancer patient populations.  Results: Vascular enrichment of the LCM samples was confirmed by Q-PCR of CD31. Hierarchical two-dimensional clustering of the transcriptome data identified 219 significantly upregulated transcripts in at least 4/8 patient samples (cut-off >1.3-fold, p<0.05). Several genes AGRN, FLNA and ILR4 were selected and their protein overexpression was confirmed in the tumor tissue. Additional mining of the data set using the clinical information associated with these tissues by applying an integrative bioinformatics network method generated a 15-gene ‘Vascular-Derived Prognostic Predictor’ that is able to stratify patient populations in to high- and low- risk groups.  Conclusions: The overall heterogeneity observed in the vascular gene expression patterns in the infiltrating ductal carcinoma samples poses a significant problem for these individual genes to be used as a robust vascular breast cancer specific marker or therapeutic target. Using an integrative bioinformatics network approach allowed us to identify a 15-gene ‘Vascular-Derived Prognostic Predictor’ that can robustly identify patients with an increased risk of local recurrence. Stratifying patient populations using this gene signature may lead to better patient-tailored treatment regimes.

overall_design: Two-color microarrays comparing laser-captured microvessels from the tumors and matching adjacent normal tissues of 8 breast cancer patients

first: Phuong

middle: U

last: Le

last: Cantin

first: Catherine

last: Collins

first: Maureen

last: O’Connor-McCourt

first: Anne

middle: E

last: Lenferink


title: Opaque filamentation in Low Phosphate (LP) and Sorbitol (SOR) compared to in SCD

city: Providence

first: Richard

last: Bennett

state: RI

address: 171 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

summary: Act1-Wor1 strain (the opaque strain CAY2903 with constitute WOR1 expression), wildtype white (a/a RBY717); Opaque hyphal formation in liquid LP and SOR compared to SCD; white cells in the same conditions as control.

overall_design: 6 condition experiment: opaque and white cells in LP, SOR and SCD. Used the pool of all conditions as reference.

first: Haoyu

last: Si


city: Wageningen

first: Ruud

last: de Maagd

address: PO Box 619

institute: Plant Resarch International

summary: Gene expression in three stages of ripening tomato fruit (variety Ailsa Craig) was determined with the EUTOM3 Affymetrix array in order to compare with degradrome sequencing data from study GSE42661, treated as RNAseq.

overall_design: three replicates of each stage (MG, mature green; T, turning/breaker; RR, red ripe) were hybridized; Expression values were normalized for each sample and reported by iTAG2.3 cDNA identifier in the accompanying matrix table.

first: Arnaud

last: Bovy


title: microRNA expression profiles in androgenetic, parthenogenetically activated and fertilized embryonic stem cells

city: Cheongju

first: Nam-Hyung

last: Kim

state: Chungbuk

address: Gaeshin-dong

institute: Chungbuk National University

summary: In this study, miRNA expression profiles were examined by Illumina microarray in mouse embryonic stem cells (ESCs) derived from androgenetic (aESC), parthenogenetic (pESC) and fertilized (fESC) blastocysts. Results showed that 125, 42 and 99 miRNAs were differentially expressed in the aESCs vs. fESCs, pESCs vs. fESCs and aESCs vs. pESCs, respectively.

overall_design: Androgenetic, parthenogenetically activated and fertilized embryonic stem cell lines were established from androgenetic and fertilized blasotocyst. microRNA microarrays were repeated three times using passages 6, 7 and 8.

first: Xiang

last: Cui

first: Teruhiko

last: Wakayama

first: Nam


title: Gene expression profiles in liver of F344 rat treated with chemical

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

institute: Chemicals Evaluation and Research Institute, Japan

summary: The rodent carcinogenicity test requires extremely long test term and large examination cost. Therefore, now we need to develop a short term and low cost screening method. We already developed a chemical carcinogenicity short term  screening method CARCINOscreen®. This study was performed to validate this screening method.  We conducted 28 days-repeated dose experiments in male F344 rats with 4 carcinogens and 2 non-carcinogens, and the gene expression profiles in liver were measureed by custom oligo microarrays.

overall_design:
Two-condition experiment, control vs. chemical treated rat liver. Biological replicates: 4 control, 4 treated, control samples were pooled. One replicate per array.
Compound treatments:
4 carcinogens: Hexachloroethane, 1,2,3-Trichloropropane, 1-Amino-2-methylanthraquinone, 3-(4-Chlorophenyl)-1,1-dimethylurea
2 non-carcinogens: 1,2-Dichlorobenzene and Tetracycline hydrochloride

first: Fumiyo

last: Saito

first: Masahiro

last: Takeyoshi


title: Evaluation of hepatic gene expression profiles during androgen exposure in female mosquitofish

city: Gainesville

first: Erica

middle: Karin

last: Brockmeier

state: FL

address: 2187 Mowry Road

institute: University of Florida

summary: The Eastern Mosquitofish (Gambusia holbrooki) is a non-model species with the potential for development of biomarkers of endocrine disrutpting chemical (EDC) exposure due to its androgen-driven secondary sexual characteristics. While G. holbrooki have been utilized in the field as bioindicator organisms EDC exposure in areas impacted by pulp and paper mills, the lack of molecular tools and general understanding of how G. holbrooki are impacted by androgen exposure hinder the use of this organism as a widespread tool for the evaluation of these chemicals in the environment. While traditional gene-by-gene approaches have provided a list of genes that may be appropriate for developing into biomarkers of androgen exposure, a more inclusive method could provide more rapid and expansive determination of genes that can be developed into biomarkers of androgen exposure. The objective of this study is toutilize a mosquitofish microarray to determine potential biomarkers of chronic androgen exposure. The specific aim was to determine genes that may be developed into biomarkers of chronic androgen exposure in hepatic tissues using 17β-trenbolone (TB) exposed adult female G. holbrooki by microarray analysis.

overall_design: Liver tissues from a 14-day exposure of female G. holbrooki to 1 µg/L of the potent androgen receptor agonist 17β-trenbolone (17β-hydroxyestra-4,9,11-trien-3-one; abbreviated as TB) [Brockmeier 2013] were used as the first sample for microarray analysis using the custom G. holbrooki microarray to determine genes that were significantly up or down-regulated during a chronic androgen agonist exposure. RNA was isolated from the livers as previously described using TRIzol (Invitrogen, Grand Island, USA), hydrated using RNAsecure (Ambion, Grand Island, USA), and DNase treated using the Turbo DNA-free kit (Ambion, Grand Island, USA). Four oocyte-development stage-matched RNA samples per treatment were evaluated for RNA integrity using the 2100 BioAnalyzer (Agilent, Santa Clara, USA). The range of RIN values was 8.3-8.9.

first: Nancy

last: Denslow


title: array-CGH on single blastomeres from day-4 human preimplantation fresh and frozen embryos

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

institute: Vrije Universiteit Brussel

summary: In total, 240 single blastomeres from nine top-quality day-4 embryos frozen at day 3 of development and four fresh top-quality day-4 embryos that had one-cell biopsy on day 3 for preimplantation genetic diagnosis (PGD) were collected. Blastomeres' DNA was amplified using SurePlex DNA Amplification System (BlueGnome, Cambridge, UK) . Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome, www.cytochip.com).

overall_design: BAC array-CGH on single blastomeres amplified by SurePlex amplification Kit.

first: Afroditi

last: Mertzanidou

first: Hilde

last: Van De Velde

first: Karen

last: Sermon


title: Baseline serum anti-glycan antibodies of 113 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine [Validation Total Ig 1:200]

city: Frederick

first: Christopher

last: Campbell

state: MD

address: 376 Boyles Street

institute: NCI

summary:
Purpose: There is evidence that therapeutic cancer vaccines can lengthen survival for some cancer patients, but responses vary widely from one person to another.  Methods to predict clinical outcomes will advance the field and provide new insights into critical determinants of in vivo efficacy.  This study uses a high-throughput glycan microarray to assess correlations between a subject's overall survival after receiving PROSTVAC-VF and his baseline serum anti-glycan antibody levels.
Results:  Pre-vaccination antibody levels to blood group A trisaccharide (BG-Atri) were found to have a statistically significant correlation with survival.  Long-term survival was approximately doubled in subjects with abundant anti-BG-Atri IgM relative to subjects with little or no pre-existing IgM for BG-Atri.  This survival correlation was specific to vaccine treatment, as no correlation was observed in control patients immunized with wild-type poxviruses lacking the key tumor antigen, prostate specific antigen (PSA).  Moreover, anti-BG-Atri IgM levels were not correlated with general measures of disease severity, such as PSA levels, Gleason score, or Halabi predicted survival.
Conclusion: In addition to reporting a new potentially predictive biomarker for PROSTVAC-VF, this study highlights the potential of glycan microarray technology for personalized medicine.

platform_organism:
Quercus alba
Gossypium hirsutum
Medicago sativa
Rhodotorula
Pandalus borealis
Gallus gallus
Homo sapiens
Bos taurus
Ovis aries
Mus musculus
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  Total immunoglobin (IgM + IgG + IgA) levels for the validation set measured at serum dilution of 1:200 are detailed here.  The screen for predictive biomarkers identified anti-glycan antibodies that consistently stratified subjects into groups with different Kaplan Meier survival estimates.  Due to the potential for overfitting, a permutation test was used to estimate the false discovery rate.
Raw data on superSeries GSE42184 record.

middle: T

first: James

middle: L

last: Gulley

first: Oyindasola

last: Oyelaran

middle: W

last: Hodge

first: Jeffrey

last: Schlom

middle: C

last: Gildersleeve


title: Baseline serum anti-glycan antibodies of 28 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine  [Training Total Ig 1:200]

platform_organism:
Quercus alba
Gossypium hirsutum
Rhodotorula
Pandalus borealis
Gallus gallus
Homo sapiens
Bos taurus
Ovis aries
Mus musculus
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  Total immunoglobin (IgM + IgG + IgA) levels for the training set measured at serum dilution of 1:200 are detailed here.  The screen for predictive biomarkers identified anti-glycan antibodies that consistently stratified subjects into groups with different Kaplan Meier survival estimates.  Due to the potential for overfitting, a permutation test was used to estimate the false discovery rate.
Raw data on superSeries GSE42184 record.


title: Transcriptome Analysis from non-alcoholic steatohepatitis (NASH)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: The mechanisms underlying the progression of non-alcoholic steatohepatitis (NASH) are not completely elucidated. In this study we have integrated gene expression profiling of liver biopsies of NASH patients with translational studies in a mouse model of steatohepatitis and with pharmacological interventions in isolated hepatocytes to identify a novel mechanism implicated in the pathogenesis of NASH. By using high-density oligonucleotide microarray analysis we identified a significant enrichment of known genes involved in the multi-step catalysis of long chain polyunsaturated fatty acids, including delta-5 and 6 desaturases. A combined inhibitor of delta-5 and delta-6 desaturases significantly reduced intracellular lipid accumulation and inflammatory gene expression in isolated hepatocytes. Gas chromatography analysis revealed impaired delta-5 desaturase activity toward the omega-3 pathway in livers from mice with high-fat diet (HFD)-induced NASH. Consistently, restoration of omega-3 index in transgenic fat-1 mice expressing an omega-3 desaturase, which allows the endogenous conversion of omega-6 into omega-3 fatty acids, produced a significant reduction in hepatic insulin resistance, hepatic steatosis, macrophage infiltration and necroinflammatory liver injury, accompanied by attenuated expression of genes involved in inflammation, fatty acid uptake and lipogenesis.  These results were comparable to those obtained in a group of mice receiving a HFD supplemented with EPA/DHA. Of interest, hepatocytes from fat-1 mice or supplemented with EPA exhibited synergistic anti-steatotic and anti-inflammatory actions with the delta-5/ delta-6 inhibitor. Conclusion: These findings indicate that both endogenous and exogenous restoration of the hepatic balance between omega-6 and omega-3 fatty acids and/or modulation of desaturase activities exert preventive actions in NASH.

overall_design: The complete database comprised the expression measurements of   18185 genes for liver  sample groups: 8 non-alcoholic steatohepatitis (NASH ) and  7 control samples.

first: C

last: López-Vicario

first: J

last: Claria


title: DNA methylation in normal PC, MGUS, SMM and MM

status: Public on Apr 03 2013

city: Bronx

first: Christoph

last: Heuck

address: 1300 Morris Park Ave

department: Cancer Center

institute: Albert Einstein College of Medicine

type: Methylation profiling by genome tiling array

summary: To characterize epigenomic changes during the transformation of normal plasma cells to myeloma, we used the HELP assay to analyze the methylome of CD138+ cells from 56 subjects representing premalignant (MGUS), early and advanced stages of  myeloma as well as healthy controls. Plasma cells from premalignant and early stages of myeloma were characterized by striking, widespread hypomethylation.

overall_design: CD138+ selected bone marrow plasma cells from 8 normal donors, 11 patients with monoclonal gammopathy of uncertain significance (MGUS), 4 patients with smoldering myeloma (SMM), 13 patients with newly diagnosed myeloma (NEWMM), 16 patients with relapsed myeloma (REL), including 2 patients with serial samples,  and 2 patients in clinical complete remission (REM) were analyzed using the HELP assay [HpaII tiny fragment Enrichment by Ligation-mediated PCR].

first: Amit

last: Verma

first: Seema

last: Singhal


title: Drug-induced hepatotoxicity screening in primary mouse hepatocytes, an Omics approach.

city: Maastricht

first: Anke

last: Van Summeren

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

summary: Drug-induced hepatotoxicity is a leading cause of attrition of candidate drugs in drug development. Therefore new screening methods are necessary which predict these hazards more accurate and earlier in the drug development process. Of all in vitro hepatotoxicity models, primary human hepatocytes are considered as 'the gold standard'. However, the use of these hepatocytes is hindered by their scarcity and major inter-individual variation. These limitations may be overcome with use of primary mouse hepatocytes. Within this context changes in protein expressions in primary mouse hepatocytes, after exposure to cyclosporin A were studied using differential gel electrophoresis. Thereafter, the mRNA expression levels of these deregulated proteins from cyclosporin A-treated cells were analyzed. Cyclosporin A induced ER stress and altered the ER-Golgi transport, which may alter vesicle mediated transport and protein secretion. Moreover are the differentially expressed proteins observed upon challenge by cyclosporin A, associated with cholestatic mechanisms.

overall_design: For each biological experiment, one hybridization was conducted and one sample per array. In total, 6 arrays were used for 2 different conditions (Csa or control at 48 hours).

first: Johan

last: Renes

first: Daneida

last: Lizarraga

first: Freek

last: Bouwman

first: Jean-Paul

last: Noben

first: Joost

last: van Delft

first: Jos

last: Kleinjans

first: Edwin

last: Mariman


title: Baseline serum anti-glycan antibodies of 113 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine [Validation Total Ig 1:50]

first: Christopher

last: Campbell

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  Total immunoglobin levels (IgM + IgG + IgA) for the validation set measured at serum dilution of 1:50 are detailed here.  The screen for predictive biomarkers identified anti-glycan antibodies that consistently stratified subjects into groups with different Kaplan Meier survival estimates.  Due to the potential for overfitting, a permutation test was used to estimate the false discovery rate.
Raw data on superSeries GSE42184 record.

first: James

last: Gulley

last: Oyelaran

last: Hodge


title: Expression analysis of CaMsrB2-transformed rice (Oryza sativa L. cv. ILMI) without/with Bar selection marker under drought stress conditions

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

summary: Methionine sulfoxide reductases catalyze the reduction of MetSO back to the correct Met residue. Previously, the gene of Capsicum annuum methionine sulfoxide reductase B2 was isolated and CaMSRB2-overexpressing tomato shows enhanced growth, which may trigger increased resistance to the pathogens. To assess the role of this enzyme in rice, we generated transgenic lines under the control of the rice Rab21 (responsive to ABA protein 21) promoter with/without Bar marker gene. Several physiological tests such as MV and Fv/Fm, indicators of an oxidative stress-inducing agent and a potential maximal PSII quantum yield, respectively strongly suggested CaMSRB2 confers drought tolerance to rice. Using 3′-tiling microarray covering the whole rice genes, we carried out genome-wide expression analyses with CaMsrB2-transformed rice (Oryza sativa L. cv. ILMI).  Rice was grown in port for six weeks and treated with drought by water withholding for two days.

overall_design: A total of 15 chips were used for the microarray experiment.  RNA was extracted from plants just before and 2 days after the duration of water withdrawal for the control and the comparison, respectively. Experiments were performed with three or two biological replicates.

first: Joung

first: Yul-Ho

first: Hyang-Mi

last: Park

first: Baek

last: Nahm


title: Baseline serum anti-glycan antibodies of 28 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine [Training Total Ig 1:50]

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  Total immunoglobin (IgM + IgG + IgA) levels for the training set measured at serum dilution of 1:50 are detailed here.  The screen for predictive biomarkers identified anti-glycan antibodies that consistently stratified subjects into groups with different Kaplan Meier survival estimates.  Due to the potential for overfitting, a permutation test was used to estimate the false discovery rate.
Raw data on superSeries GSE42184 record.

first: Oyindasola

first: Jeffrey

last: Schlom

last: Gildersleeve


title: Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma [aCGH_1M]

status: Public on Mar 26 2013

city: Heidelberg

first: Thomas

last: Wolf

address: Im Neuenheimer Feld 580

institute: DKFZ

summary:
Oligonucleotide aCGH profiles from 209 neuroblastoma tumor samples were generated using 44K, 105K or 1M microarrays.
The 209th sample is represented by Sample GSM634116.

overall_design: Two-color array-based comparative genome hybridization (aCGH)

first: Hayriye

last: Kocak

first: Matthias

last: Fischer

first: Jessica

last: Theissen


title: Baseline serum anti-glycan antibodies of 28 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine [Training IgM 1:50]

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  IgM levels for the training set measured at serum dilution of 1:50 are detailed here.  The screen for predictive biomarkers identified anti-glycan antibodies that consistently stratified subjects into groups with different Kaplan Meier survival estimates.  Due to the potential for overfitting, a permutation test was used to estimate the false discovery rate.
Raw data on superSeries GSE42184 record.


title: Expression data from bovine ovarian theca cells in primary culture

status: Public on Mar 15 2013

city: Reading

first: Phil

last: Knight

address: Hopkins Building, Whiteknights

country: United Kingdom

institute: University of Reading

summary: Bone morphogenetic proteins (BMP) are firmly implicated as intra-ovarian regulators of follicle development and steroidogenesis. We carried out a microarray analysis to examine global changes in gene expression in bovine theca cells in response to treatment with BMP6 alone and in combination with LH. There was a major effect of BMP6 treatment on the gene expression profile with a much weaker effect of LH. None of these differences in response to LH treatment was found to be statistically significant after applying Benjamini-Hochberg correction. BMP6 significantly (>2-fold; P<0.01) up- or down-regulated expression of 445 genes. Insulin-like peptide 3 (INSL3) was the most heavily down-regulated gene (-43-fold) with CYP17A1 and other key transcripts involved in TC steroidogenesis including LHCGR, INHA, STAR, CYP11A1 and HSD3B1 also down-regulated. BMP6 also reduced expression of NR5A1 encoding steroidogenic factor-1 known to target the promoter regions of the aforementioned genes. Real-time PCR confirmed these findings and also revealed a marked reduction in expression of INSL3 receptor (RXFP2). Secretion of INSL3 protein and androstenedione were also suppressed suggesting a functional link between BMP and INSL3 pathways in controlling androgen synthesis.

overall_design: Theca interna cells (TC) were isolated from adult bovine ovaries obtained from the slaughterhouse. TC pooled from approximately 50 individual 4-6mm follicles were plated out in in 24-well plates (0.5 x106 viable cells/ml/well) and cultured for 6 days under defined serum-free conditions with treatments present on days 3-6 inclusive. TC were treated for 4 days with BMP6 (10 ng/ml) under both basal and LH-stimulated conditions (± 160 pg LH/ml). These dose-levels of BMP6 and LH were chosen because they elicited optimal responses in our previous studies. The experiment was replicated four times with TC harvested from different batches of ovaries. Total RNA was isolated using the Ribopure RNA isolation kit (Ambion) according to the manufacturer’s instructions. RNA yield and quality were evaluated by spectrophotometry at 260/280 nm and agarose gel electrophoresis before submitting 5 μg of each RNA sample (n = 16 comprising 4 biological replicates x 4 treatment conditions) to an accredited Affymetrix service provider for microarray analysis using the bovine genome array GeneChip (n=16 arrays).

first: Raymond

last: Rodgers

first: Claire

last: Glister


title: Baseline serum anti-glycan antibodies of 113 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine  [Validation IgM 1:50]

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  IgM levels for the validation set measured at serum dilution of 1:50 are detailed here.  The screen for predictive biomarkers identified anti-glycan antibodies that consistently stratified subjects into groups with different Kaplan Meier survival estimates.  Due to the potential for overfitting, a permutation test was used to estimate the false discovery rate.
Raw data on superSeries GSE42184 record.


title: Baseline serum anti-glycan antibodies of 28 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine [Training IgG 1:50]

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  IgG levels for the training set measured at serum dilution of 1:50 are detailed here.  The screen for predictive biomarkers identified anti-glycan antibodies that consistently stratified subjects into groups with different Kaplan Meier survival estimates.  Due to the potential for overfitting, a permutation test was used to estimate the false discovery rate.
Raw data on superSeries GSE42184 record.


title: Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma [aCGH_44k]

first: Benedikt

last: Brors


title: Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma [aCGH_105k]


title: Baseline serum anti-glycan antibodies of 113 subjects in a clinical trial of PROSTVAC-VF, a therapeutic cancer vaccine [Validation IgG 1:50]

first: Christopher

last: Campbell

overall_design:
The overall study was a retrospective analysis of 141 subjects from phase II trials of PROSTVAC-VF, a poxvirus based cancer vaccine currently in phase III clinical trials for advanced prostate cancer.  The subjects were divided into a training set (n=28) and a validation set (n=113).  A glycan microarray was used to profile pre-vaccination anti-glycan antibody populations in sera as potential biomarkers for PROSTVAC-VF.  For both the training set and validation set, the anti-glycan profiles were measured using four variations of serum dilution and isotype specific secondary antibody (IgM at 1:50, IgG at 1:50, total Ig at 1:50, and total Ig at 1:200).  IgG levels for the validation set measured at serum dilution of 1:50 are detailed here.  The screen for predictive biomarkers identified anti-glycan antibodies that consistently stratified subjects into groups with different Kaplan Meier survival estimates.  Due to the potential for overfitting, a permutation test was used to estimate the false discovery rate.
Raw data on superSeries GSE42184 record.


title: MFAP4 is an integrin αVβ3/5 ligand involved in vascular remodeling

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary:
Arterial injury or occlusive arterial disease may stimulate healing responses, which when overexuberant, leads to restenosis of the injured vessel. This response is influenced by specific integrin signalling in vascular smooth muscle cells (VSMCs). Microfibril-associated protein 4 (MFAP4) colocates in blood vessels with elastic fibers. MFAP4 contains an N-terminal RGD-motiv, which is a potential integrin binding site. The role for MFAP4 in vascularproliferative disease is so far unknown and the subject for these investigations.
Here we show that MFAP4 is expressed and secreted by VSMCs and binds elastin and collagen. MFAP4 mediated adhesion, and migration, and proliferation of VSMCs in an integrin αVβ3/5 dependent manner and the effects were inhibited by MFAP4 blocking antibodies. MFAP4 deficient mutant mice were generated and appeared with a normal cardiophysiological phenotype. When challenged by carotid artery ligation, the MFAP4 deficient mice had delayed neointimal formation and the compensatory outward remodeling of the vessel diameter and thus the vessel lumen was reduced. MFAP4 expression appeared unaffected by the induced pathology.
HUMANE DATA
	This new MFAP4 mediated molecular mechanism for regulation of integrin αVβ3/5 signalling may have therapeutic implications in diseases where VSMC migration and proliferation are involved in the pathogenesis.

overall_design: For genome-wide expression analysis total RNA from heart of four male MFAP4-/- and four control mice was isolated using RNeasy Midi kit (Qiagen, Hilden, Germany). The cDNA microarrays were generated, hybridized and analysed as described (Horsch et al 2009). Two chip hybridizations were performed with total RNA for each individual mutant mouse against a reference RNA pool of the same organ.

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: The Chlamydia trachomatis plasmid-encoded Pgp4 is a transcriptional regulator of virulence associated chromosomal genes

status: Public on Feb 28 2013

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary:
Chlamydia trachomatis causes chronic inflammatory diseases of the eye and genital tract of global medical importance.  The chlamydial plasmid plays an important role in the pathophysiology of these diseases as plasmid-deficient organisms are highly attenuated.  The plasmid encodes both noncoding RNAs and eight conserved ORFs of undefined function.

To understand plasmid gene function we generated plasmid shuttle vectors with deletions in each of the eight ORFs.  The individual deletion mutants were used to transform chlamydiae and the transformants were characterized in terms of plasmid biology and transcriptional profiling.

We show that pgp1-2, -6 and -8 are essential for plasmid maintenance while the other ORFs can be deleted and the plasmid stably maintained. We further show that a pgp4 knockout mutant exhibits an in vitro phenotype similar to its isogenic plasmid-less strain in terms of abnormal inclusion morphology and lack of glycogen accumulation.  Microarray and qRT-PCR analysis revealed that pgp4 is involved in transcriptional regulation of multiple chromosomal genes; including the glycogen synthase gene glgA.  Based on our results, we propose that Pgp1 is a plasmid replicative helicase, Pgp2 is a plasmid replication protein, Pgp4 is a transcriptional regulator of virulence associated chromosomal genes, and Pgp6-8 are plasmid partitioning proteins.  These findings have important implications for understanding the plasmid’s role in chlamydial pathogenesis and the development of novel antigenically multivalent live-attenuated chlamydial vaccines.

platform_organism:
Coxiella burnetii
Rickettsia rickettsii
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: Chlamydia trachomatis wild type vs. two deletion mutants, and mock

first: Lihua

last: Song

first: John

last: Carlson

first: William

last: Whitmire

first: Laszlo

last: Kari

first: Kimmo

last: Virtaneva

first: Daniel

first: Heather

last: Watkins

first: Bing

last: Zhou

first: Gail

first: Stephen

middle: F

last: Porcella

first: Harlan

middle: D

last: Caldwell


title: Effect of Maternal Separation on DOI-induced transcriptome

city: Mumbai

first: Madhurima

last: Benekareddy

state: Maharashtra

address: 1, Homibhabha Road, Colaba

department: Department of Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

summary:
Depression is a heterogeneous disorder characterized by a wide range of symptoms, including but not restricted to increased anxiety-like behavior, altered stress responsivity, increased depressive like behavior, decreased pleasure seeking, and altered susceptibility to drugs of abuse. Adding another level of complexity to the disease is the fact that individuals differ in their susceptibility to depression. Research done over the past decade has highlighted the contribution of early life adverse experience to this individual differences in vulnerability to depression. Such studies have been done at the clinical as well as the preclinical level, where rodent and primate models of adverse postnatal environment such as Maternal Separation (MS) are used. MS involves separation of the pup from the dam for 3h every day for the first two weeks of postnatal life. The MS model has been characterized to produce long lasting anxiety-like behavior, depressive behavior and altered stress responsivity in adulthood.
While several molecular mechanisms have been hypothesized to mediate the long lasting effects of MS, the serotonin 2a receptor is an attractive candidate, given its role in regulating anxiety-like behavior. So we set out to ask if Maternal Separation alters the 5HT2a responses. In order to assay if MS alters the transcriptional targets of the 5Ht2a receptor, we use a drug that stimulates the 5Ht2a receptor, DOI. The experiment involves injecting both control and MS animals with DOI and looking at the transcriptome induced by DOI under control and MS conditions. This would help understand how the adverse early life experience MS, alters the transcriptional response of an adult rat to stimulation at the 5HT2a receptor, which is physiologically seen in conditions of stress.

overall_design:
Maternal Separation (MS) was carried out according to standard protocol. Briefly, upon birth the litters were assigned to either the control or the maternal separation group. Pups from the maternal separation litters were separated from their mother every day for a period of 3 hours from postnatal day 2 (p2) to postnatal day 14 (p14) while the control litters were left undisturbed. After p14, the maternally separated pups were left undisturbed and all litters were weaned at postnatal day 30. Experiments on adult control and MS rats were performed at postnatal day 60.

We wanted to ask if a history of adverse experience in early life like MS would alter the transcriptional response of the adult rat to the 5Ht2a agonist DOI. In order to measure the transcriptional changes induced by DOI in control and maternally separated animals, 15 rats (7 - Control and 8 - Maternally Separated) were injected i.p. with either saline or 8 mg/kg DOI. The groups included Control (Control rats injected with saline; n=3), DOI (control rats injected with 8 mg/kg DOI; n=4), MS (MS rats injected with saline, n=4) and MS+ DOI (MS rats injected with 8 mg/kg DOI, n=4). Rats were sacrificed 2 hours after the injection by decapitation. The prefrontal cortex was quickly dissected out and stored at -70 till further use. Total RNA from each rat was extracted, labeled with Cy3 and hybridized onto Agilent Custom Rat Array 8X15K (AMADID: G2509F_16352). Each biological replicate was hybridized onto one array making the total number of arrays 15.


title: Gene expression profiling of rhesus macaques vaccinated with ALVAC-SIVgpe DNA + SIVgp120 protein subunit and unvaccinated controls after challenge with SIVmac251 - 3 wks post-infection

status: Public on Mar 01 2013

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: The SIVmac251 macaque model has been used to evaluate the efficacy of vaccine for HIV. Exposure of macaques to a single high dose of SIVmac251 results in transmission of multiple viral variants, which contrasts the few HIV variants typically transmitted in humans. In here, we investigated whether the dose of SIVmac251 challenge affected vaccination efficacy and found that exposure of the immunized macaques to single high dose of SIVmac251 resulted in no vaccine efficacy, whereas exposure to a tenfold lower dose resulted in protection from SIVmac251 acquisition and protection from disease in animals that become infected. The dose of challenge did not affect the expression of inflammatory genes in the gut in acute infection, but at set point, a significant down regulation of interferon responsive genes and up regulation of genes involved in B and T-cell responses, was observed only in vaccinated animals exposed to a lower dose of SIVmac251. Accordingly, in these animals, we also found a significant correlation with vaccine induced T-cell responses and protection from disease. These data demonstrate that the evaluation of the efficacy of vaccine candidates for HIV relies on accurate modeling in macaques to better mimic HIV transmission to humans.

overall_design: A total of 31 RNA samples were hybridized on to Rhesus Affymetrix 3' Expression arrays. The study was composed of 8 vaccinated and 10 control animals subjected to a low dose challenge and 6 vaccinated and 7 control animals subjected to a high dose challenge

first: Monica

last: Vaccari

first: Brandon

last: Keele

first: Steven

last: Bosinger

first: Melvin

last: Doster

first: Zhong-Min

last: Ma

first: Justin

last: Pollara

first: Anna

last: Hryniewicz

first: Guido

last: Ferrari

first: Youngjun

last: Guan

first: Donald

last: Forthal

first: David

last: Venzon

first: Claudio

last: Fenizia

first: Tia

last: Morgan

last: Montefiori

first: Jeffrey

last: Lifson

first: Chris

last: Miller

last: Silvestri

first: Barbara

last: Felber

first: George

last: Pavlakis

first: James

last: Tartaglia

first: Genoveffa

last: Franchini


title: Streptococcus pneumoniae in a biofilm are hyper-adhesive, avirulent, and when used as a killed whole-cell vaccine confers protection against lethal challenge

city: Baltimore

first: NIKHIL

last: KUMAR

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: For Streptococcus pneumoniae, biofilms have been suggested to promote long-term colonization of the nasopharynx and contribute to the pathology of recurrent middle ear infections. To date numerous studies have investigated the contribution of specific genetic determinants for the development of pneumococcal biofilms, however, studies examining the global changes that occur during biofilm development and how they contribute to disease are lacking. Using Scanning and Transmission electron microscopy we examined development of a mature pneumococcal biofilm in a continuous flow through reactor. We determined that a mature biofilm is formed in discrete stages, is marked by the formation of complex 3-dimensional structures, and is primarily composed of dead pneumococci. Using genomic microarrays we determined that pneumococci in mature biofilms down regulate genes involved in protein synthesis, energy production, metabolism, capsular polysaccharide production, and virulence. We confirmed these changes by testing bacterial resistance to antimicrobials, measuring capsule production by ELSIA, and immunoblotting for pneumolysin production. We determined that biofilm pneumococci are hyper-adhesive, binding to cell lines at levels 9 to 11-fold greater than planktonic counterparts. Using Western blot and ELISA, we determined that biofilm bacteria produce greater amounts of the adhesins PsrP, CbpA, and surface exposed phosphorylcholine. We subsequently determined that the hyper-adhesive phenotype was in part due to selection of the transparent phase variant during biofilm growth. Intranasal, intratracheal and intraperitoneal challenge of mice with biofilm and planktonic pneumococci determined that biofilm bacteria were highly attenuated for invasive disease but not nasopharyngeal colonization. Immunization of mice with ethanol-killed biofilm pneumococci of serotype 4 conferred protection against challenge with same isolate but not a serotype 3. ELISA for reactive IgG levels subsequently determined that biofilm pneumococci do not provide high levels of cross-reactive protein antigens. Together these studies suggest that biofilms do not directly contribute to disease but instead confer a protected mode of growth for the pneumococcus.

overall_design:
Pneumococcal biofilms compared to planktonic control at 4, 12, 24, 48 hours. 3 biological replicates each of 4 and 12 hour time points, and 2 biological replicates each of 24 and 48 hour time points.  Flip dye (technical replicates) performed for 4, 12, and 24 hour time points; no technical replicate performed for 48 hour time point due to limiting material.  Ratios were determined by averaging across technical and biological replicates.
The following hybridizations made up each biological replicate:
14090167.tav.annot and 14090190.tav.annot (4hr biol rep 1);
14090169.tav.annot and 14090176.tav.annot (4hr biol rep 2);
14090192.tav.annot and 14090188.tav.annot (4hr biol rep 3);
14087688.tav.annot and 14090180.tav.annot (12hr biol rep 1);
14090185.tav.annot and 14090168.tav.annot (12hr biol rep 2);
14090191.tav.annot and 14090174.tav.annot (12hr biol rep 3);
14090170.tav.annot and 14090175.tav.annot (24hr biol rep 2);
14090193.tav.annot and 14087687.tav.annot (24hr biol rep 3);
14090181.tav.annot (48hr biol rep 1);
14090187.tav.annot (48hr biol rep 2)

first: Carlos

last: Sanchez

first: Nikhil

last: Kumar

first: Pooja

last: Shivshankar

first: Anel

last: Lizcano

first: Julie

last: Hotopp

last: Jorgensen

first: Hervé

last: Tettelin

last: Orihuela