title: Identification of Myc target genes in xenograft tissue derived from human lung cancers

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary: All three transforming members of the Myc family play a significant role in the development of both SCLC and NSCLC. NSCLC constitutes 80% of all lung cancer, and cMyc expression is most often deregulated, compared with N-Myc and L-Myc, in this disease. Thus, although we are interested in understanding the regulation and function of the entire Myc family in all lung cancers, we focused our research on cMyc deregulation in NSCLC. To identify target genes whose regulatory regions are bound in response to deregulated cMyc in NSCLC, we analyzed mouse xenograft tumours established in immune-compromised mice from monolayer cell lines derived from primary adenocarcinoma NSCLCs. These xenografts were chosen for further study because they show a genetic profile similar to their respective primary tumour (MGH8, RVH6849, A549, MGH24). High c-myc expression positively correlates with the ability of NSCLC cell lines to form xenografts, suggesting that Myc contributes towards the ability of the cells to grow in vivo. We conducted Myc-specific ChIP-chip and the corresponding normal IgG control using the Agilent genome-wide oligonucleotide promoter arrays on 3 biological replicates, of each of the four xenograft tumours. Following pre-processing using variance-stabilizing normalization and statistical analysis using general linear models we identified a list of 2,207 genes significantly enriched for c-Myc binding.

overall_design: ChIP on Chip, Four lung xenograft cell-lines, each with n=3 with each replicate being a separate mouse

first: Romina

last: Ponzielli

first: Igor

last: Jurisica

first: Linda

middle: Z

last: Penn


title: HeLa cell response to overexpression of wild type and mutated forms of the P19 splice variant of c-H-ras

status: Public on Dec 30 2009

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

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

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

summary:
The c-H-ras proto-oncogene undergoes alternative splicing of the exon termed IDX giving rise to a novel protein of the Ras family, p19 (H-RasIDX). The experiment tests the effect on the transcriptome of overexpressing the wild type and W164A mutated forms of p19.

Keywords: genetic modification

overall_design: Three-condition experiment, where wild type p19 H-ras transfection or transfection with a mutated form (p19W164A) were compared to transfection with the negative control (empty pRK5 expression vector) which was used as the common reference. Biological replicates: 3 of each set of treatments, independently grown and harvested. Two technical replicates with dye swapping per comparison.

first: Maria

last: Camats

first: George

middle: A

last: Calin

first: Kate

middle: J

last: Heesom

first: Chang-Gong

last: Liu

first: Stefano

last: Volinia

first: Carlo

middle: M

last: Croce

first: Cristian

last: Taccioli

first: Michael

last: Ladomery

first: Montse

last: Bach-Elias


title: Genome-wide characterization of the transcriptional program of Myc-dependent transformation, ChIP-chip

status: Public on Nov 24 2009

country: Canada

type: Genome binding/occupancy profiling by array

summary:
We profiled Myc binding in a normal breast cell-line (MCF10A) under basal conditions after ectopic expression of Myc. We showed that ectopic Myc expression increases tumour formation in vivo and in vitro. We then profiled genome-wide Myc binding using Agilent promoter arrays in MCF10A cells expressing wild-type and ectopic Myc. We show that Myc binds to a greater number of spots in wild-type than in Myc cells, but that some targets are unique to each condition.

Keywords: ChIP-chip

overall_design: We compared ectopic Myc to wild-type cells with n=10 per condition

first: Amanda

middle: R

last: Wasylishen


title: Transcriptome analysis of rat soleus muscle after altered loading state and somatic overexpression of FAK

status: Public on Dec 31 2009

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

country: Switzerland

institute: University of Berne

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

overall_design: Refer to individual Series


title: Genome-wide characterization of the transcriptional program of Myc-dependent transformation

summary:
We profiled Myc binding in a normal breast cell-line (MCF10A) under basal conditions after ectopic expression of Myc. We showed that ectopic Myc expression increases tumour formation in vivo and in vitro. We then profiled genome-wide Myc binding using Agilent promoter arrays in MCF10A cells expressing wild-type and ectopic Myc. We show that Myc binds to a greater number of spots in wild-type than in Myc cells, but that some targets are unique to each condition.

This SuperSeries is composed of the SubSeries listed below.


title: DNA methylation in infant ALL

status: Public on Nov 23 2009

city: Rotterdam

first: Dominique

last: Stumpel

address: Dr. Molewaterplein 50-room Ee15-14

department: Pediatric Oncology/ Hematology

country: Netherlands

institute: Erasmus MC _ Sophia Children's Hospital

type: Methylation profiling by genome tiling array

summary:
The aggressive MLL-rearranged leukemias are well-known for their unique gene-expression profiles. The goal of this study was to characterize the MLL-specific DNA methylation profiles in infant acute lymphoblastic leukemia (ALL). Genome-wide DNA methylation profiling was performed on primary infant ALL samples. The majority of infant ALL samples demonstrated severe DNA hypermethylation compared with normal pediatric bone marrows, which implies that targeting of DNA methylation may be an interesting option for future therapeutic strategies in MLL-rearranged infant ALL.
Using ALL cell lines carrying the MLL translocation t(4;11) (SEMK2 and RS4;11) as a model for the patient cells, we demonstrated that the hypermethylated genes are sensitive to demethylation.

overall_design: DNA methylation profiling was performed on t(4;11)-positive (n=16), t(11;19)-positive (n=15), t(9;11)-positive (n=6) and untranslocated (n=12) infant ALL samples compared with whole normal bone marrow samples (n=7). Cell lines SEMK2 and RS4;11 were profiled with and without the demethylating agent zebularine.

first: Ronald

middle: W

last: Stam

first: Pauline

last: Schneider


title: Effect of TCPOBOP, PCN, rosuvastatin, and atorvastatinin on cholesterol homeostasis

status: Public on Nov 20 2009

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana


title: Effects of salt stress on Medicago truncatula seedlings

status: Public on Nov 11 2009

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

country: USA

institute: Washington University in St. Louis

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula


title: Comparative Analysis of Genes Induced by Respiratory Syncytial Virus and DsRNA in Human Epithelial Cells

status: Public on Nov 16 2009

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Epithelial cells are the primary target of respiratory viral infections and play a pivotal role in virus-induced lung inflammation and in anti viral immune response. A common signal for the presence of viral infections and induction of inflammation is recognition of double stranded RNA (dsRNA). Thus far, there has not been a high-throughput transcrptome analysis of RSV- or dsRNA-induced genes in primary human bronchial epithelial cells (PHBE), nor there has been a comparison between dsRNA- and RSV-induced genes. To establish the transcriptome profiles and to determine the contribution of dsRNA in the induction of inflammation during respiratory virus infection, we compared the gene expression profiles of PHBE cells that were infected with RSV or were treated with dsRNA. Our transcriptome analysis showed that RSV infection and and dsRNA treatment induced up-regulation of 2024 and 159 genes in PHBE respectively.  Comparison of genes revealed that RSV and dsRNA commonly induced 80 genes in PHBE cells. The common up-regulated genes were functionally grouped in multiple response pathways involved in inflammation and immune responses. Interestingly, there were several previously unreported genes that were up-regulated in primary human epithelial cells that are relevant to a TH2 allergic phenotype. This comparison of a high-throughput gene expression study offers a comprehensive view of transcriptional changes induced by dsRNA and RSV, and importantly compares dsRNA-induced genes with RSV-induced genes in PHBE cells.

overall_design:
Primary human bronchial epithelial cells were left untreated, were treated with 1 ug/ml dsRNA (poly I:C), or were infected with RSV at multiplicity of infection (MOI) of 2.5 plaque forming unit (pfu)/cell.  After 2 hr for dsRNA and 24 hr for RSV, total cellular RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturers’ instructions.
Gene expression analysis was conducted using Agilent Human1Av2 arrays two color system (Agilent Technologies, Palo Alto, CA).  Dye swap were performed to eliminate dye bias. Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol.  For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.  Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v7.5 and 9.1), using defaults for all parameters.

first: Gino

middle: V

last: Limmon

first: Kelly

middle: L

last: McCann

first: Danica

last: Andrews

first: Farhad

last: Imani


title: Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA

status: Public on Nov 10 2009

city: Stanford

first: Patrick

middle: O

last: Brown

state: CA

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine

type:
Other
Expression profiling by array


title: Androgen repsonsive microRNAs

status: Public on Nov 01 2009

city: Baltimore

first: Shawn

middle: E

last: Lupold

state: MD

address: 600 N Wolfe St

department: Urology

institute: Johns Hopkins University School of Medicine

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: miRNA profiling from freshly harvested duodenums and livers

status: Public on Oct 30 2009

city: Heidelberg

first: Mirco

last: Castoldi

address: Im Neuenheimer Feld 156

department: Department of Pediatric Oncology, Hematology and Immunology

country: Germany

institute: University of Heidelberg


title: Comparative gene expression analysis between Nipponbare and 6-4 under two conditions

status: Public on Oct 31 2009

city: Tsukuba

first: Matthias

last: Wissuwa

address: 1-1 Ohwashi

country: Japan

institute: JIRCAS

summary:
Nipponbare performs poorly in phosphorus (P) deficient soil whereas a Nipponbare-derived NIL containing the Pup1 allele of donor parent Kasalath is tolerant to P deficiency. In this experiment we compared gene expression patterns in roots of this NIL to Nipponbare, grown either in a P deficient or P fertilized soil. The aim is to separate constitutive differences in expression from those induced by P deficiency.
Keywords: genotype comparison, constitutive differential expression

overall_design:
Total RNA was extrancted from root that were grown under two conditions and prepared three biological replicant in each line (total 6 samples in each line).
We used 6 slides for this experiment, in each slide, Nipponbare and 6-4 samples grown under same condition were hybridized.

first: JP

last: Tanaka

first: K

last: Maruyama

last: Satoh


title: Comparisons of caruncles, intercaruncles, AI, IVF-ET and SCNT in pregnancies

city: Jouy-en-Josas

first: Olivier

last: Sandra

address: Domaine de Vilvert

department: UMR BDR

country: France

institute: INRA


title: SMAD1/5, SMAD2 and SMAD4 binding/occupancy profiling in murine embryonic stem cells R1

status: Public on Oct 21 2009

city: Beijing

first: Bing

last: Zhou

address: Datun Road

department: Center for Molecular Systems Biology

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary:
To determine the binding targets of SMAD1/5, SMAD2 and SMAD4 in mouse ESCs, ChIP combined with DNA microarray was carried out according to Agilent Mammalian ChIP-on-chip protocol. Briefly, immunoprecipitated (IP) DNA was blunted with T4 polymerase and ligated to linkers with T4 DNA ligase. For reference, 200 ng of input DNA was used. Ligated DNA was amplified with two rounds of PCR cycles. Two ug of each amplified sample were labeled with Cy5 for IP DNA, and Cy3 for input DNA using CGH labeling kit (Invitrogen). Four ug of each labeled sample was blocked with mouse Cot-1 DNA (Invitogen) and blocking agent (Agilent), and hybridized to DNA microarrays (G4490A, Agilent) for 40 h at 65℃. The microarrays were washed and stabilized with acetonitrile (Sigma), followed by stabilization and drying solution (Agilent). The arrays were scanned with Agilent DNA microarray scanner (G2565BA), and probe features were extracted using Feature Extraction Software (version 10.0). The raw data were processed by the R package limma and the log-ratio of IP over WCE was normalized within arrays using ‘loess’ method. And the normalized log-ratios were then used for SMAD target selection. Bound targets which was determined by the algorithm was validated by ChIP-stie specific PCR on a selected number of genes. The false positive rate was determined.
Keywords: ChIP-chip

overall_design: ChIP assay were carried out in undifferentiated murine R1 ES cells and extracted DNA were analyzed by Agilent Mouse Promoter two-color Array(G4490A) according to manufacturer’s instruction.  Anti-SMAD1/5 antibody generated with recombinant human SMAD1-linker (aa145-267)-His, Anti-SMAD2 antibody generated with recombinant human SMAD2-linker and Anti-SMAD4 antibody generated with recombinant human SMAD4-linker (aa144-316)-His were used for ChIP assay.   Biological replicates: 1 SMAD1/5 replicate, 1 SMAD2 replicate and 1 SMAD4 replicate.

first: Teng

last: Fei

first: Kai

last: Xia

first: Shanshan

last: Zhu

first: Hua

last: Chen

first: Zhongwei

first: Jianping

last: Zhang

first: Zhang

first: Huasheng

last: Xiao

first: Jing-Dong

last: Han

first: Ye-Guang


title: ChIP-chip with antibodies for histone 3 lysine 4 trimethylation and histone 3 in Mll1+/+ and Mll1-/- MEFs

status: Public on Oct 20 2009

city: Kansas City

first: Pengfei

last: Wang

address: 1000 E. 50th Street

institute: Stowers Institute

summary:
Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II

A common landmark of activated genes is the presence of trimethylation on lysine 4 of histone H3 (H3K4) at promoter regions.  The Set1/COMPASS was the founding member and the only H3K4 methylases in S. cerevisiae, however, in mammals at least six H3K4 methylases Set1A/B and MLL1-4 are found in COMPASS-like complexes capable of methylating H3K4. To gain further insight into the different roles and functional targets for the H3K4 methylases, we have undertaken a genome-wide analysis of H3K4 methylation pattern in wild-type Mll1+/+ and Mll1-/- mouse fibroblasts (MEFs).  We found that Mll1 is required for the H3K4 trimethylation of less than 5% of promoters   carrying this modification.  Many of these genes, which include developmental regulators such as Hox genes show decreased levels of RNA polymerase II recruitment and   expression concomitant with the loss of H3K4 methylation. Although Mll1 is only required for the methylation of a subset of Hox genes, Menin, a component of the Mll1   and Mll2 complexes, is required for the overwhelming majority of H3K4 methylation at Hox loci.  However, the loss of MLL3/4 and/or the Set1 complexes have little to no effect   on the Hox loci H3K4 methylation or expression levels in these MEFs.  Together these data provide insight into redundancy and specialization of COMPASS-like complexes in   mammals and provide evidence on a possible role for Mll1-mediated H3K4 methylation in the regulation of transcriptional initiation.

overall_design: Chromatin Immunoprecipitation was performed with antibodies for histone 3 lysine 4 trimethylation and histone 3 in Mll1+/+ and Mll1-/- mouse embryonic fibroblasts. Two biological replicates were done. DNA for all four samples was hybridized to the commercially available Agilent Mouse Promoter array, a two-array set that tiles mouse promoters genome-wide.

first: Chengqi

last: Lin

first: Edwin

last: Smith

first: Hong

last: Guo

first: Brian

last: Sanderson

first: Min

last: Wu

first: Madelaine

last: Gogol

first: Tara

last: Alexander

first: Christopher

last: Seidel

first: Leanne

last: Wiedemann

last: Ge

first: Robb

last: Krumlauf

first: Ali

last: Shilatifard


title: Autonomous plasmid-like replication of a conjugative transposon

status: Public on Oct 16 2009

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

summary:
Integrative and conjugative elements (ICEs), a.k.a., conjugative transposons, are mobile genetic elements involved in many biological processes, including the spread of antibiotic resistance. Unlike conjugative plasmids that are extra-chromosomal and replicate autonomously, ICEs are integrated in the chromosome and replicate passively during chromosomal replication. It is generally thought that ICEs do not replicate autonomously. We found that when induced, Bacillus subtilis ICEBs1 replicates as a plasmid. The ICEBs1 origin of transfer (oriT) served as the origin of replication and the conjugal DNA relaxase served as the replication initiation protein. Autonomous replication of ICEBs1 conferred genetic stability to the excised element, but was not required for mating. The B. subtilis helicase PcrA that mediates unwinding and replication of Gram-positive rolling circle replicating plasmids was required for ICEBs1 replication and mating. Nicking of oriT by the relaxase and unwinding by PcrA likely directs transfer of a single-strand of ICEBs1 into recipient cells.

This SuperSeries is composed of the SubSeries listed below.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Refer to individual Series.


title: AI-2 does not function as a quorum sensing molecule in Campylobacter jejuni during exponential growth in vitro

status: Public on Oct 08 2009

city: Dublin

first: Kathryn

last: Holmes

address: Trinity Centre for Health Science, Adelaide and Meath Hospital

department: Clinical Medicine

country: Ireland

institute: Trinity College Dublin

platform_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819


title: Microarray analysis of CL-20 reversible neurotoxicity in the earthworm Eisenia fetida

status: Public on Oct 14 2009

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC

summary: The earthworm Eisenia fetida is one of the most used species in standardized soil ecotoxicity tests. Endpoints such as survival, growth and reproduction are ecologically relevant but provide little mechanistic insight into the toxicity pathways, especially at the molecular level. To better understand toxicological modes of action and to facilitate the development of molecular biomarkers, we have obtained 30,245 unique EST sequences from E. fetida and have designed a novel microarray with 15,119 60-mer oligonucleotide probes. These probes target the unique non-redundant EST sequences identified in E. fetida. Using this array we have profiled gene expression of E. fetida after exposure to CL-20, a cage cyclic nitramine previously found exhibiting reversible neurotoxicity to worms. Worms were exposed for 6 days to CL-20. Half of the exposed worms were allowed to recover in a clean environment for 7 days. Electrophysiological analysis showed that the conduction velocity of worm medial giant nerve fiber was significantly decreased after 6-d exposure to CL-20, and that giant nerve fiber function was restored at the end of the 7-d recovery period. Total RNA samples isolated from four treatment groups (6 replicates per group), i.e., 6-d control, 6-d exposed, 13-d control and 6-d exposed with 7-d recovery, were analyzed using the new 15K oligo array. Bioinformatics and statistical analyses have identified specific neurological pathways affected by CL-20 and recovery of these pathways after CL-20 removal. These results provide significant insights on the CL-20 toxic mode of action and how earthworms can recover from chemical stressors.

overall_design: Adult earthworms (E. fetida) were exposed on filter paper to CL-20 (0.2 ug/cm2) for 6 days with or without 7-day recovery (4 treatment groups in total). Each treatment group had 9 replicate worms, six of which were used for gene expression analysis. Worms were measured for their medial giant nerve fiber conduction velocity using a non-invasive electrophysiological technique immediately before takedown. At the termination of the 6-d or 13-d experiment, worms were snap-frozen and fixed in RNAlater-ICE. Total RNA was isolated from the fixed worms. A total of 24 worm RNA samples were hybridized to three 8x15K custom-designed Agilent oligo arrays using Agilent’s one-color Low RNA Input Linear Amplification Kit. The array contains 15,208 non-redundant 60-mer probes, each targeting a unique E. fetida transcript. After hybridization and scanning, gene expression data were acquired using GenePix Pro 6.0.

first: Xin

last: Guan


title: Genes expressed in salivary glands and gut of Hessian fly larvae are likely involved in interactions with host plants

status: Public on Oct 06 2009

city: Manhattan

first: Ming

last: Chen

state: KS

address: Kansas State University, 123 Waters Hall

department: Entomology

institute: Kansas State University


title: Histone H1 binding is restricted by histone variant H3.3

status: Public on Oct 15 2009

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by genome tiling array


title: Altered gene expression and DNA damage in peripheral blood cells from Friedreich's ataxia patients

status: Public on Dec 08 2009

first: NIEHS

last: Microarray Core

summary:
Frataxin, a conserved mitochondrial protein involved in iron homeostasis, is reduced in patients with Friedreich’s ataxia (FRDA).  Transcription profiling and DNA damage assays were performed on blood cells from FRDA patients.  Altered expression patterns pertained to immune response, signaling pathways, transcription, apoptosis, and genotoxic stress response pathways.  FRDA patients had significantly more mitochondrial and nuclear DNA damage than a control population.  Frataxin mRNA levels correlated with age of onset and displayed unique sets of gene alterations involved in oxidative phosphorylation and protein synthesis.  Thus analysis of blood in FRDA patients yields insight into the nature and progression of the disease, as well as potential therapeutic approaches.
Keywords: Friedreich's ataxia; frataxin; mitochondrial DNA damage; nuclear DNA damage; genotoxic stress

overall_design:
Peripheral blood samples were collected from 48 children with FRDA participating in a randomized, placebo-controlled clinical trial for idebenone.  All whole blood samples in this study were collected before administration of idebenone.  RNA was isolated utilizing the PAXgene™ blood RNA isolation kit (PreAnalytiX/ QIAGEN, Hilden, Germany) according to the manufacturer’s protocol, including the optional on-column DNase digestion, except that the centrifugation time after proteinase K digestion was increased from 3 to 20 minutes in order to obtain a tighter debris pellet.  RNA quality was assessed with an Agilent Bioanalyzer™ (Palo Alto, CA) to ensure that samples with intact 18S and 28S ribosomal RNA peaks were used for microarray analysis.  Twenty samples were lost during the isolation procedures with 28 high-quality RNA samples remaining.  RNA was also isolated, using the same methods already described, from 14 FRDA adults and 15 healthy adults as controls.  Lymphoblastoid FRDA cell line and age-matched control RNAs were isolated using the QIAGEN Rneasy midi (100–500 µg RNA) according to the manufacturer’s protocol.
Gene expression profiling was conducted using Agilent Human 1A(V2)  Oligo arrays  with ~20,000 genes represented (Agilent Technologies, Palo Alto, CA).  Each sample was hybridized against a human universal RNA control (Stratagene, La Jolla, CA). 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit, according to manufacturer’s protocol.  For each two color comparison, 750 ng of each Cy3- (universal control) and Cy5-labeled (sample) cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner (Agilent Technologies, Wilmington, DE). The data were obtained with the Agilent Feature Extraction software (v9.1), using defaults for all parameters. The Feature Extraction Software performs error modeling before data are loaded into a database system.  Images and GEML files, including error and P values, were exported from the Agilent Feature Extraction software and deposited into Rosetta Resolver (version 5.0, build 5.0.0.2.48) (Rosetta Biosoftware, Kirkland, WA).

first: Astrid

last: Haugen

first: Nicholas

last: DiProspero

first: Joel

middle: S

last: Parker

first: Rick

middle: D

last: Fannin

first: Jeff

last: Chou

middle: N

last: Meyer

last: Halweg

first: Jennifer

middle: B

last: Collins

first: Alexandra

last: Durr

first: Kenneth

last: Fischbeck

first: Bennett

last: VanHouten


title: Effect of auxin (indole-3-acetic acid) on chicken DT40 cells

status: Public on Oct 01 2009

city: Toyonaka

first: Masato

last: Kanemaki

state: Osaka

address: Machikaneyama 1-1,

department: Department of Biological Sciences,

institute: Osaka University

summary: DT40 cells and a stable DT 40 cell line expressing OsTIR1 (clone 9) were treated with 500µM IAA for 6 hours.  This experiment was conducued to see if auxin would induce a specific sets of genes in animal, like it does for plant cells.  We didn't observe a significant difference between the mock control and IAA  treatments in both DT40 cells and the stable cells.

overall_design: Exponentially growing DT40 cells or stable DT40 cells expressing OsTIR1 were treated with 500µM IAA for 6 hours.  This experiment was conducued to see if auxin would induce a specific sets of genes in animal, like its does for plant cells.

first: Kohei

last: Nishimura


title: Time course of bacteriophage ϕYS40 infection in wild-type and crp deletion Thermus thermophilus HB8 strain

status: Public on Nov 03 2009

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

first: Yoshihiro

last: Agari

first: Keiko

last: Sakamoto

first: Aimi

last: Osaki

first: Miwa

last: Ohmori

first: Seiki

last: Kuramitsu


title: Non-small Cell Lung Cancer (qRT-PCR)

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases


title: Mature vs immature microfilariae

city: Oshkosh

first: Kathryn

last: Griffiths

state: WI

address: 800 Algoma Blvd

department: Biology and Microbiology

institute: University of Wisconsin Oshkosh

summary:
Filarial nematodes are arthropod-borne nematodes that cause a variety of economically important diseases such as onchocerciasis (river blindness), lymphatic filariasis, and heartworm disease.  The most widespread filarial disease of humans is lymphatic filariasis, caused by worms in the genera Wuchereria and Brugia. Lymphatic filariasis is an economic and social burden in endemic countries and affects approximately 119 million people worldwide (Michael, 1997). In humans, the worms live in and block the lymph vessels, causing improper flow of lymph, and inflammation of the lymphatic system. The symptoms are fever, swollen limbs and genitals, generalized malaise, and can progress to a debilitating condition known as elephantiasis
This research focuses on the transmission of these worms to the disseminating mosquito host, and it is based on the interesting observation that mf must be at least 7 days old to successfully infect the mosquito (de Hollanda, 1982). Newborn mf that have not ‘matured’ cannot successfully penetrate the midgut of the mosquito, and subsequently cannot develop to the L3 stage (Fuhrman, 1987). Previous work done by another group 20 years ago suggests that the molecular makeup of the worm surface changes during this maturation process (Furman, 1983 a and b).  We used microarray analysis to characterize changes in gene expression that take place during the mf maturation process. Understanding the gene expression changes that occur as the mf mature will allow us to understand the nature of the philological transition that allows mf to move from the human to the mosquito host. With this information in hand, we can eventually identify parasite molecules that could be targeted to either stop parasite reproduction or prevent transmission of the mf to the mosquito. This would stop parasite transmission in endemic areas.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Brugia malayi
Brugia pahangi

first: George

last: Mayhew

first: Rebecca

last: Zink

first: Sara

last: Erickson

first: Jeremy

last: Fuchs

first: Bruce

last: Christensen

first: Colleen

last: McDermott

first: Michelle

last: Michalski


title: Bovine Hypertrophic Growth Plate Chondrocytes vs. Reserve Zone Chondrocytes

status: Public on Oct 27 2009

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Growth plate chondrocytes were isolated from the distal metacarpus of young dairy cattle (all under 10 mo of age), the chondrocytes were released from the extracellular matrix by digestion with Collagenase P for 4 hours, and the various zones of the growth plate were separated by density centrifugation. The least-dense Hypertrophic Zone (HZ) cells were compared to the most-dense Reserve Zone (RZ) cells. 6 pairs of HZ vs RZ were compared by microarray.

overall_design: Growth plate chondrocytes were isolated from the distal metacarpus of young dairy cattle (all under 10 mo of age), the chondrocytes were released from the extracellular matrix by digestion with Collagenase P for 4 hours, and the various zones of the growth plate were separated by density centrifugation. The least-dense Hypertrophic Zone (HZ) cells were compared to the most-dense Reserve Zone (RZ) cells.  Six independent sample pairs of HZ vs RZ were compared by microarray.

first: Michele

last: Hutchison

first: Mary

middle: H

last: Bassett

first: Perrin

last: White


title: Transcriptional changes in the secretome of S. mansoni during early development and in the presence of erythrocytes

status: Public on Oct 02 2009

city: Herston

first: Alex

middle: P

last: Loukas

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR

summary: We have examined the gene expression profile of the transformation of the blood fluke Schistosoma mansoni  from the cercarial to schistosomula stages. Specifically cercariae were mechanically transformed and then cultured for 3 hours or 5 days, and then total RNA was isolated and microarray analysis performed. A second experiment compares the effect that the presence of red blood cell in the culturing conditions has over the 3 hour and 5 day periods have on the parasite.

platform_organism:
Schistosoma japonicum
Schistosoma mansoni

overall_design: Agilent custom designed microarray was used. One colour experimental design. One biological replicate was labelled and then two technical replicates (hybridisations) performed for each sample. A total of 5 samples were examined, cercariae, 3 hrs +RBCs, 5 days + RBCs, 3 hrs –RBCs and  5 days – RBCs.

first: Geoffrey

last: Gobert

first: Mai

last: Tran

first: Luke

last: Moertel

first: Malcolm

middle: K

last: Jones

first: Donald

last: McManus


title: Expression profiling of murine hemopoietic cell survival

status: Public on Sep 26 2009

city: Adelaide

first: Anna

last: Tsykin

state: SA

address: Frome Road

department: Hanson Institute

institute: SA Pathology


title: Induction of the IL-6/signal transducer and activator of transcription pathway in the lungs of mice exposed to tobacco

status: Public on Sep 14 2009

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

summary:
We have examined the impact of subchronic levels of tobacoo smoke on murine lungs. We have used high density DNA microarray and analysed lung tissues from mice exposed to mainstream tobacco smoke (MTS). Our results reveal induction of inflammatory cytokine interleukin-6 (IL-6) and its antagonist suppressor of cytokine signalling (SOCS3) mRNA in smoking group. We also show that these changes are transient and are reversed completely after a period of cessation of smoking.

Keywords: Toxicology, disease state analysis, biomarkers of health effects

overall_design: Male C57B1/CBA mice were exposed to MTS from two cigarettes daily, 5 days/week for 6 or 12 weeks. Mice were sacrificed immediately, or six weeks following the last cigarette. Left lung lobes were removed and flash frozen. Total RNA was isolated from a small part of the frozen lung and was hybridized against universal mouse reference RNA to Agilent Oligo DNA microarrays (Agilent Technologies) containing 22,000 transcripts. Microarrays were normalized using a global LOWESS approach and analyzed by MAANOVA 2.0 and SAM. Microarray results were validated by real time RT-PCR. Impact of alteration in expression of select genes was further validated by analysing their total protein levels in lung tissue homogenates.

first: Sabina

last: Halappanavar

first: Marsha

last: Russell

first: Martin

last: Stampfli

first: Carole

last: Yauk


title: Oogenesis in Solea senegalensis: various developmental stages

city: Talence

first: angela

last: tingaud-sequeira

address: avenue des Facultés

institute: Université Bordeaux 1


title: Genetic characterization of tumor-stage mycosis fungoides

status: Public on Sep 15 2009

city: Barcelona

first: Rocio

last: Salgado

address: Passeig Marítim, 25-29

institute: IMIM-Hospital del Mar

type: Genome variation profiling by genome tiling array

summary: Mycosis fungoides patients who develop tumors or extracutaneous involvement usually have a poor prognosis with no curative therapy available so far. In the present EORTC multicenter study, the genomic profile of 41 skin biopsies from tumor-stage mycosis fungoides was analyzed using a high-resolution oligo-array comparative genomic hybridization platform. Seventy-six percent of cases showed genomic aberrations. The most common imbalances were gains of 7q33.3q35 followed by 17q21.1, 8q24.21, 9q34qter and 10p14 and losses of 9p21.3 followed by 9q31.2, 17p13.1, 13q14.11, 6q21.3, 10p11.22, 16q23.2 and 16q24.3. Three specific chromosomal regions, 9p21.3, 8q24.21 and 10q26qter were defined as prognostic markers exhibiting a significant correlation with overall survival (P= .042, P= .017 and P= .022, respectively). Moreover, we have established two MFt genomic subgroups distinguishing a stable group (0-5 DNA aberrations) and an unstable group (> 5 DNA aberrations), showing that the genomic unstable group had a shorter overall survival (P=.05). We therefore conclude that specific chromosomal abnormalities, such as gains of 8q24.21 (MYC) and losses of 9p21.3 (CDKN2A, CDKN2B and MTAP), and 10q26qter (MGMT and EBF3) may play an important role in prognosis.  In addition, we describe the MFt genomic instability profile.

overall_design: Forty-one MFt were studied by arrayCGH using the Human Genome CGH 44K microarrays (G4410B and G4426B, Agilent Technologies, Palo Alto, CA, USA). In each microarray experiment, DNA obtained from a 20x10 um sections snap frozen samples from tumoral MF lesions was compared with commercial pools of healthy female DNA (Promega, Madison, WI, USA).

first: Octavio

last: Servitje

first: Fernado

last: Gallardo

first: Maarten

last: Vermeer

first: Pablo

last: Ortiz-Romero

first: Maria

last: Karpova

first: Marie

middle: C

last: Zipser

first: Cristina

last: Muniesa

last: Garcia-Muret

first: Teresa

last: Estrach

first: Marta

last: Salido

first: Julia

last: Sanchez-Schmidt

last: Herrera

first: Vicenç

last: Romagosa

first: Javier

last: Suela

first: Bibiana

middle: I

last: Ferreira

first: Juan

last: Cigudosa

first: Carlos

last: Barranco

first: Sergi

last: Serrano

first: Reinhard

last: Dummer

first: Cornelis

last: Tensen

first: Frances

last: Solé

first: Ramon

last: Pujol

first: Blanca

last: Espinet


title: Role of stpA in Salmonella typhimurium

status: Public on Oct 28 2009

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

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

first: Paul

last: McDermott

first: Arthur

last: Thompson

first: Jay

last: Hinton


title: Human airway inflammatory cell response to LPS and house dust mite antigen

city: RTP

first: John

last: Tomfohr

address: 111 T.W. Alexander Dr. P.O. Box 12233

institute: NIEHS

summary:
Allergic asthmatic, allergy only, asthma only (no allergy), and non-allergic non-asthmatic (control) subjects underwent bronchoscopy with instillation of saline, lipopolysaccharide (LPS), and house dust mite antigen in separate subsegmental bronchi. Bronchoalveolar lavage (BAL) fluid was collected four hours later (three samples per subject). Inflammatory cells from each specimen were isolated and RNA was extracted for microarray analysis.
Keywords: gene expression arrays (two-dye: sample against common 'universal' reference RNA)

overall_design:
There are four main phenotypic groups:
1. control (no allergy or asthma)
2. allergy only (no asthma)
3. asthma only (no allergy)
4. allergy and asthma
and three exposures: saline, house dust mite antigen (HDM), and LPS.

Samples from the different exposures were all collected at the same time: four hours after instillation. The hybridizations were carried out in two main 'batches': samples in batch 1 were processed in mid 2004, samples in batch 2 about a year later in 2005. There is a clear 'batch effect': differences between expression profiles from the two batches (likely caused by technical differences between hybridization and scanning methods). This should be considered when analyzing the data.

first: J

last: Singh

last: Sundy

first: K

last: Foss

first: E

last: McElvania-Tekippe

first: I

last: Yang

first: D

last: Schwartz


title: The Aryl Hydrocarbon Receptor Regulates Tissue-Specific Dioxin-Dependent and Dioxin-Independent Gene Batteries

status: Public on Sep 18 2009

city: Toronto

last: Boutros

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

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

first: Kirsten

middle: A

last: Bielefeld

first: Raimo

last: Pohjanvirta

first: Patricia

last: Harper


title: C. briggsae and C. elegans developmental timecourses

status: Public on Aug 31 2009

city: Haifa

first: Itai

last: Yanai

address: Technion City

country: Israel

institute: Technion - Israel Institute of Technology

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans


title: DnaN overexpressing cells and YabA-null cells

status: Public on Sep 01 2009

city: Cambridge

first: Alan

last: Grossman

address: 31 Ames Street, 68-530

institute: MIT

type:
Expression profiling by array
Genome variation profiling by array


title: Mice with fibrinogen-induced arthritis (FIA)

status: Public on Sep 12 2009

city: Stanford

first: William

last: Robinson

address: 269 Campus Dr

institute: Stanford University

platform_organism:
Homo sapiens
Mus musculus


title: Characterisation of the NRF2-mediated anti-oxidant gene battery by transcriptional profiling

status: Public on Aug 30 2009

city: Dunee

first: simon

middle: matthew

last: plummer

state: Angus

address: 2 James Lindsay Place

department: CXR

institute: CXR Biosciences ltd

summary:
Transcriptional profiling in HACAT cells using a whole human genome array
HACAT cells treated with si RNA against Keap 1 or a scrambled si RNA sequence (Scram) vs HACAT cells mock transfected with lipofectamine (reference control)

overall_design: 2 biological replicates, 2 technical (dye swap) replicates per treatment.

first: Simon

last: Plummer

last: Hayes


title: The comparison of CpG methylation profiles between CD34+ and CD34- human umbilical cord blood cells

status: Public on Aug 29 2009

city: Seoul

first: Il-Hoan

last: Oh

address: Banpo-Dong, Socho-Gu

department: Institute of Cell and Gene Therapy

country: South Korea

institute: The Catholic University of Korea, Medical College

summary: Evidence for the epigenetic regulation of hematopoietic stem cells (HSCs) is growing, but the genome-wide epigenetic signature of HSCs and its functional significance remain unclear. In this study, we used high-resolition (Agilent, CpG Island ChIP-on-chip) platforms for genome-wide comparison of CpG methylation in human CD34+ and CD34- cells.

overall_design: CD34+ and CD34- cells were purified from human umbilical cord blood. Genomic DNA obtained from CD34+ and CD34- cells was fragmented by either sonication or digestion with MseI. Recombinant methyl-binding domain (Genomictree, Daejeon, Korea) was incubated with sonicated genomic DNA in a binding reaction mixture. The methyl-enriched DNA fraction was purified using Qiaquick PCR purification kits (Qiagen, Hilden, Germany) and amplified using a whole genome amplification kit as recommended by Agilent. Amplified DNA products from CD34+ and CD34- cells were labeled with Cy3-dUTP and Cy5-dUTP, respectively, by random priming and hybridized onto Agilent human CpG island microarrays using conditions specified by the manufacturer (Agilent, Santa Clara, CA). After washing, the slides were scanned using an Agilent scanner and images were quantified using the Feature Extraction Software v. 9.3 (Agilent).


title: Variation in germline gene expression in cde-1 mutant

city: Utrecht

first: Rene

last: Ketting

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: analysis of germline gene expression in wildtype and cde-1 mutant C. elegans.

overall_design: Worms were staged, gonads were dissected in Trizol, and RNA was isolated, all using standard protocols. The series includes a young adult and an aged adult sample, and a dye swap of both. In most respects the two stages can be regarded as duplicates.

first: Josien

last: van Wolfswinkel

middle: F

first: Eugene

last: Berezikov


title: Development of a novel parameter for quantification of methylation levels in MeDIP-CpG island microarray analysis

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center Research Institute

summary: Microarray analysis of DNA methylation has a great promise in biomedical research.  However, its accuracy in quantification of DNA methylation, especially at intermediate levels, is still unreliable due to the lack of an appropriate parameter that takes account of unique distribution nature of methylation levels and highly variable mean methylation levels depending upon individual samples.  Here, for methylated DNA immunoprecipitation-microarray analysis, we developed a parameter, "Me value" as a parameter that linearly correlates with methylation levels in CpG islands (CGIs) in various samples with various mean methylation levels.  The Me value had a linear correlation with the fraction of methylated DNA molecules obtained by bisulfite sequencing (R=0.86).  Analysis of cells treated with 5-aza-2'-deoxycitidine showed that distribution of the Me values shifted toward lower methylation levels.  For analysis of completely unmethylated or methylated CGIs, common threshold values stood valid with accuracy of 80 % for cell lines with various methylation levels, which was shown by methylation-specific PCR of more than one hundred loci.  Combined with expression microarray analyses, it was shown that methylation of promoter CGIs was significantly associated with low gene expression while that of far downstream was not.  It was also shown that various regions against TSSs are demethylated evenly by a demethylating agent, and that the degree of demethylation of any region was not associated with the degree of re-expression.

overall_design: Genome-wide methylation analysis of six samples were performed using MeDIP and CpG island microarray.  Analysis of AGS was replicated for checking reproducibility.

first: Kosuke

last: Hosoya

first: Ken

last: Gyobu

first: Monali

last: Lahoti

first: Toshikazu

last: Ushijima


title: Hepatocellular carcinoma (HCC) in FEAT transgenic mouse

city: Fukuoka

first: Atsushi

last: Takahashi

address: 3-1-1, Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: Transgenic mice (n= 40) overexpressing FEAT in the thymus, spleen, liver, and lung developed malignant lymphoma (47.5%, 19/40) and liver cancer (hepatocellular carcinoma, HCC) (35%, 14/40).  Notably, HCC arose in half (13/26) of the male transgenic mice, indicating a strong male predilection similar to human HCC.  Microarray-based comparative genomic hybridization (array-CGH) suggested that HCC in FEAT transgenic mice recapitulates human hepatocarcinogenesis.

overall_design: DNA labeling and hybridization to 244k slide format 60-mer oligonucleotide microarrays for array-CGH (Agilent Mouse Genome CGH Microarray Kit 244A) were performed using genomic DNA from mouse HCCs as experimental samples and genomic DNA from the liver of a normal C57BL/6 mouse as a reference sample.   The microarrays were scanned using a Micro Array Scanner, and data were extracted using Feature Extraction software and analyzed using CGH analytics 3.4 software according to the manufacturer's instructions (Agilent Technologies).

first: Hisashi

last: Tokita

first: Miki

last: Ohira

first: Akira

last: Nakagawara


title: Changes in gene expression in gamma delta T cells induced by Yamoa

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

state: MT

address: 960 Technology Blvd.

department: Veterinary Molecular Biology

institute: Montana State University

summary:
Yamoa™ is marketed and sold as a dietary supplement with anecdotal positive effects in asthma and hay fever.  We determined that Yamoa™ (ground bark of Funtumia elastica tree) stimulated innate immunity in part by affecting gamma delta T cells.  Yamoa™ had distinct priming effects, very similar to, but more robust than, that of lipopolysaccharide (LPS), on bovine, mouse and human gamma delta T cells.  However, the optimal effect was dependent on the presence of accessory cells.  Gene expression patterns in bovine gamma delta T cells and monocytes induced by Yamoa™ were very similar to those induced by ultrapure LPS, but the agonists in Yamoa™ did not signal entirely through TLR4.  Yamoa™ stimulated human cells to produce cytokines involved innate protection.  The bioactive component of Yamoa™ was delineated to a complex polysaccharide fraction (Yam-I).  Intraperitoneal injection of Yamoa™ and very low doses of Yam-I in mice induced rapid increases peritoneal neutrophils directed by changes chemokine expression.  Yamoa™ and Yam-I were effective as therapeutic treatments in mice with Salmonella enterica serotype Typhimurium (ST) induced enterocolitis that resulted in decreased bacterial counts in feces.  This initial characterization of the immune stimulatory properties of polysaccharides derived from Yamoa™ suggests potential mechanisms for positive effects in asthma and that they have potential for application in infectious disease settings. .

Keywords: comparison of 3 treatment types, LPS, Yamoa, innate, adjuvant

overall_design: To begin to understand the effects of Yamoa in innate immunity, we investigated the global gene expression profiles of stimulated bovine gamma delta T cells.  Peripheral blood from 3 neonatal bovine calves was collected.  gamma delta T cells were sorted to >97% purity using a FACS Vantage.  Cells were placed in culture and stimulated with either an aqueous extract of Yamoa (32.6ug/ml), ultrapure LPS [uLPS (10ug/ml)] or PBS for 4 hours after which RNA was extracted and processed for microarray analysis.

first: Jill

last: Graff


title: Microarray between Normal and SMAR1 overexpression B16F10 cells

status: Public on Aug 25 2009

city: Pune

first: samit

last: chattopadhyay

state: Maharashtra

address: University of Pune Campus

country: India

institute: National Centre for Cell Science

summary: The present microarray studies the differential transcription levels of various genes upon overexpression of tumor suppressor protein SMAR1. The results will lead us to potential targets which are either up/downregulated by SMAR1.

overall_design: Agilent two-color experiment,Organism: Human ,Slides, Agilent’s Human Microarray G4110B with 22000 features, Labeling kit: Agilents Low input RNA linear amplification Kit Cat # 5184-3523, Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA

first: Devraj

last: Mogare

first: Archana

middle: J

last: Badhwar

first: Kamini

last: Singh

first: L

last: Pavithra

first: Surajit

last: Sinha

first: K

last: Sreenath

first: Sunil

last: Malonia

first: Sandeep

first: Samit

last: Chattopadhyay


title: A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

type: Expression profiling by genome tiling array

type: Non-coding RNA profiling by genome tiling array

overall_design: Refer to individual Series


title: Renal gene expression analysis of rat malignant hypertensive end-organ damage

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: University of Edinburgh

summary:
Severe forms of hypertension are characterized by high blood pressure combined with end-organ damage. Through the development and refinement of a transgenic rat model of malignant hypertension (MH) incorporating the mouse renin gene, we previously identified a quantitative trait locus (QTL) on chromosome 10, which affects malignant hypertension severity and morbidity. We next generated an inducible MH model where the timing, severity and duration of hypertension was placed under the control of the researcher, allowing development of and recovery from end-organ damage to be investigated. We have now generated novel consomic Lewis (L) and Fischer (F) rat strains with inducible hypertension, and additional strains, which are reciprocally congenic for the refined chromosome 10 QTL – FL (Fischer with a Lewis congenic region and LF (Lewis with a Fischer congenic region). We have captured a modifier of end-organ damage within the QTL and, using a range of bioinformatic, biochemical and molecular biological techniques, have identified Angiotensin converting enzyme (Ace) as the modifier of tissue microvascular injury.

This SuperSeries is composed of the SubSeries listed below.

overall_design: 48 samples: 4 strains (F, L, FL, LF) x 3 time points (0, 7, 10 day induction) x 4 biological replicates each


title: Human umbilical vein endothelial cells (HUVECs) treated with fenofibrate

status: Public on Aug 24 2009

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

institute: University of Cambridge


title: Novel endogenous antisense transcripts in mouse

city: Tsukuba

first: Koji

last: Numata

address: 3-1-1 Koyadai

institute: RIKEN

overall_design:
Refer to individual Series

Unpublished data has been masked in the supplementary feature extraction files.


title: Expression profiling of the host and the Ovine Herpesvirus 2 pathogen during malignant catarrhal fever of cattle

status: Public on Aug 01 2009

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

institute: ETH Zurich / University of Zurich

platform_organism:
Bos taurus
Ovine gammaherpesvirus 2


title: Expression profiling of Bos taurus lymph nodes upon infection with Ovine Herpesvirus 2

summary:
We hypothesized that the relative abundances of host cell transcripts in lymph nodes of animals with malignant catarrhal fever (MCF), compared to healthy controls, may be used to identify pathways that may help to explain the pathogenesis of MCF. Therefore, an abundance of host cell gene expression patterns in lymph nodes of animals with MCF and healthy controls were analyzed by microarray. Indeed, a vast number of genes related to inflammatory processes, lymphocyte activation, cell proliferation and apoptosis were detected at different abundances. However, the IL-2 transcript was eminent among the transcripts, which were, compared to healthy controls, less abundant in animals with MCF. Compared to healthy cattle, bovines with MCF appear to mimic an IL-2 knockout phenotype that has been described in mice. This supports the hypothesis that immunopathogenic events are linked to the pathogenesis of MCF. IL-2-deficiency may play an important role in the process.

Keywords: disease state analysis

overall_design: Comparison of lymph node samples from 3 infected animals with lymph node samples from 6 uninfected animals.

first: Claudia

last: Meier-Trummer

first: Andrea

last: Patrignani

first: Ulrich

last: Wagner

first: Mathias

last: Ackermann


title: Comparison of expression in PAM765-transgenic vs GUS-transgenic Arabidopsis

status: Public on Jul 30 2009

city: Bunkyo

first: Kenro

last: Oshima

institute: The University of Tokyo

summary: PAM765 encodes the secretory protein of a phytopathogenic bacterium, Candidatus Phytoplasma asteris. To investigate the influence of PAM765 expression on the transcription profile of a host plant, we identified differences in the gene expression profiles between PAM765-transgenic and GUS-transgenic Arabidopsis plants using microarray analysis.

overall_design: Three independent transgenic lines were harvested from 2-week-old tengu- or GUS-transgenic plants, and were used for microarray analysis.

first: Ayaka

last: Hoshi

first: Shigeyuki

last: Kakizawa

first: Yoshiko

last: Ishii

first: Johji

last: Ozeki

first: Masayoshi

last: Hashimoto

first: Ken

last: Komatsu

first: Satoshi

last: Kagiwada

first: Yasuyuki

last: Yamaji

first: Shigetou

last: Namba


title: Microarray analyses of high Arctic soil bacterial response to hydrocarbon pollution and bioremediation

status: Public on Aug 07 2009

city: Montreal

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

institute: NRC-BRI

type:
Expression profiling by array
Other

sample_organism:
Bacteria
Escherichia coli
Archaea

platform_organism: Bacteria Archaea


title: Analysis of spatial mRNA expression differences in the skin of Casp-8F/–K5-Cre or Casp-8F/+K5-Cre mice

status: Public on Jul 29 2009

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

summary: Expression of enzymatically inactive caspase-8, or deletion of caspase-8 from basal epidermal keratinocytes, triggers chronic skin inflammation in mice. Unlike similar inflammation resulting from arrest of NF-kB activation in the epidermal cells, the effect induced by caspase-8 deficiency did not depend on TNF, IL1, dermal macrophage function, or expression of the Toll-like receptor adapter proteins MyD88 or TRIF. Both interferon regulatory factor (IRF)3 and TANK-binding kinase were constitutively phosphorylated in the caspase-8-deficient epidermis, and knockdown of IRF3 in the epidermis-derived cells from these mice abolished the expression of upregulated genes. Temporal and spatial analyses of the alterations in gene expression that result from caspase-8 deficiency reveal that the changes are initiated before birth, around the time that cornification develops, and occur mainly in the suprabasal layer. Finally, we found that caspase-8-deficient keratinocytes display an enhanced response to gene activation by transfected DNA. Our findings suggest that an enhanced response to endogenous activators of IRF3 in the epidermis, presumably generated in association with keratinocyte differentiation, contributes to the skin inflammatory process triggered by caspase-8 deficiency.

overall_design: Total RNA was extracted from the dermis or epidermis derived from Casp-8F/–K5-Cre and Casp-8F/+K5-Cre mice at P3. RNA from two or three mice of each genotype was pooled prior to sample processing for microarray analysis. The appropriate pairs of RNA samples suited for a direct comparison of the two different genotypes under examination were differently labeled and subsequently co-hybridized onto one microarray (dual color design).

first: Andrew

last: Kovalenko

first: Jin-Chul

last: Kim

first: Tae-Bong

last: Kang

first: Akhil

last: Rajput

first: Konstantin

last: Bogdanov

first: Michael

last: Kracht

first: Ori

last: Brenner

first: David

last: Wallach


title: Global survey of miRNA profiles in the uterus and an estrogen receptor alpha knockout embryo

status: Public on Jul 22 2009

city: bukyo-ku

first: kaoru

last: yamagata

address: yayoi 1-1-1

institute: university of tokyo

first: Kaoru

last: Yamagata

first: Shigeaki

last: Kato


title: Evolved polymorphism in E. coli

status: Public on Jul 25 2009

city: Missoula

first: Frank

last: Rosenzweig

address: 32 Campus Drive, HS 104

department: Division of Biological Sciences

institute: University of Montana

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


title: Identification of mRNAs modulated by knockdown of CD24 and enriched in G3BP immunoprecipitation

status: Public on Jul 23 2009

city: Nankoku

first: Keisuke

last: Taniuchi

address: Kohasu, Oko

institute: Kochi University Medical School


title: Rhodospirillum rubrum S1H Space Flight Experiments

status: Public on Jun 30 2009

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

country: Belgium


title: Expression profiling of skeletal muscle in beef cattle treated with steroidal growth promoters

status: Public on Jul 07 2009

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

summary: In the present study, a oligonucleotide microarray platform is used to compare expression profiles of beef cattle muscle in animals treated with either Dexamethazone (Dex) or Dexamethazone plus 17β-estradiol (Estr) administered at sub-therapeutic dosage, against untreated controls. Seventeen male beef cattle 15-18 months old, around 450 kg mean body weight were randomly allocated in three groups: 6 were untreated (group Ctrl), 5 were administered with dexamethazone via feed 0.75mg/head for 43 days (group D); the last 6 animals were administered via feed for 43 days with Dex (0.75mg/head) and intramuscularly (i.m.) for three times with 17β-oestradiol, 20mg/head, (group DE). Three additional control animals, matching in sex and age, collected in a previous experiment were included in the Ctrl group to increase sample size and to control for biological variation. For each sample, total RNA was extracted from a specific anterior limb muscle (biceps branchii). Data analysis demonstrates that the expression profiles were strongly affected by Dex treatment with hundreds of genes up-regulated with relevant fold-change, whereas the myostatin gene was significantly down-regulated. On the contrary, the administration of Dex-Estr reveals a weaker effect on gene expression.

overall_design: In this study, we analyzed the gene expression profiles of 20 anterior limb muscle samples, 9 collected from untreated controls, 5 collected from cattle treated with Dex and 6 from cattle treated with Dex+Estr using Agilent-015354 Bovine oligo microarray platform (20 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays  are scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides are scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal

first: Lisa

last: Carraro

first: Barbara

last: Cardazzo

first: Luca

last: Bargelloni


title: Gene expression profiles of serous ovarian cancer samples

status: Public on Jul 19 2009

city: Niigata

first: Kosuke

last: Yoshihara

address: 1-757 Asahimachi-dori

department: Obstetrics and Gynecology

institute: Niigata University

summary: To elucidate the mechanisms of rapid progression of serous ovarian cancer, gene expression profiles from forty-three ovarian cancer tissues comprising eight early stage and thirty-five advanced stage tissues were performed using oligonucleotide microarrays of 18,716 genes. By non-negative matrix factorization analysis using 178 genes, which were extracted as stage-specific genes, 35 advanced-stage cases were classified into two subclasses with superior (n = 17) and poor  (n = 18) outcome evaluated by progression-free survival (logrank test, p = 0.03). Of the 178 stage-specific genes, 112 genes were identified as showing different expression between the two subclasses. Of the 48 genes selected for biological function by Gene Ontology analysis or Ingenuity Pathway Analysis, 5 genes (ZEB2, CDH1, LTBP2, COL16A1 and ACTA2) were extracted as candidates for prognostic factors associated with progression-free survival. The relationship between high ZEB2 or low CDH1 expression and shorter progression-free survival was validated by real-time RT-PCR experiments of 37 independent advanced-stage cancer samples. ZEB2 expression was negatively correlated with CDH1 expression in advanced-stage samples, whereas ZEB2 knockdown in ovarian adenocarcinoma SKOV3 cells resulted in an increase in CDH1 expression. Multivariate analysis showed that high ZEB2 expression was independently associated with poor prognosis. Furthermore, the prognostic effect of E-cadherin encoded by CDH1 was verified using immunohistochemical analysis of an independent advanced-stage cancer samples set (n = 74). These findings suggest that the expressions of epithelial-mesenchymal transition-related genes such as ZEB2 and CDH1 may play important roles in the invasion process of advanced-stage serous ovarian cancer.

overall_design: Forty-three serous ovarian cancer samples were analyzed. Ten normal peritoneum samples were used as controls.

first: Atsushi

last: Tajima

first: Dai

last: Komata

first: Tadashi

last: Yamamoto

first: Shoji

last: Kodama

first: Hiroyuki

last: Fujiwara

first: Mitsuaki

last: Suzuki

first: Yoshitaka

last: Onishi

first: Masayuki

last: Hatae

first: Kazunobu

last: Sueyoshi

first: Hisaya

first: Yoshiki

last: Kudo

first: Ituro

last: Inoue

first: Kenichi

last: Tanaka


title: Ginger and Turmeric microarray in different tissues at different developmental stages

status: Public on Jul 09 2009

city: Tucson

first: David

middle: R

last: Gang

state: AZ

address: 1657 E Helen Street

department: Plant Sciences

institute: The University of Arizona

sample_organism:
Zingiber officinale
Curcuma longa

platform_organism:
Zingiber officinale
Curcuma longa


title: Gene Expression Analysis of Carbonyl Sulfide Neurotoxicity

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: To gain insight into the pathogenesis of carbonyl sulfide induced neurotoxicity, we examined the gene expression profile of exposed rats before the onset of morphological changes (days 1 and 2) using the most consistently affected brain region, the posterior colliculus.

overall_design: Immediately after the cessation of COS exposure on the appropriate day of sacrifice (day 1 or day 2) the rats were deeply anesthetized with intraperitoneal sodium pentobarbital. The posterior colliculi were surgically exposed and removed using a pair of corneal scissors and fine forceps. The samples were immediately placed in RNase-free plastic vials and snap frozen in liquid nitrogen. Three control animals (non-exposed) were processed identically.  Total RNAs from frozen brain tissue (posterior colliculus) were isolated with an RNeasy tissue kit (Qiagen, Valencia, CA) according to the manufacturer's protocols. The quality and integrity of the RNA was verified by 260/280 nm absorbance ratio, formaldehyde agarose gel electrophoresis and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Gene expression analysis was conducted using Agilent Rat Oligo Microarrays (Agilent Technologies, Palo Alto, CA).  Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol.  For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.  Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.  Two arrays were utilized for each comparison allowing for dye reversals.  Data was obtained using the Agilent Feature Extraction software (v8.1), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).

first: James

last: Morrison

first: Kiki

last: Ton

first: Jennifer

last: Collins

first: Robert

last: Switzer

first: Peter

last: Little

first: Daniel

last: Morgan

last: Sills


title: Expression Profiling of Genes Concerning to Protective Effect in Heart by Benidipine Hydrochloride.

status: Public on Jun 16 2009

city: Asahi-machi, Machida-shi

first: Ayako

last: Kawabata

department: BioFrontier Laboratories

institute: Kyowa Hakko Kogyo co.,LTD.

summary:
Benidipine hydrochloride is a long-acting calcium channel blocker and is used for the treatment of hypertension and angina pectoris. The cardioprotective effects of benidipine have been shown in several animal and clinical studies. We examined the effect of the dihydropyridine calcium channel blocker (CCB) benidipine on the gene expression profile in heart by DNA microarray.
Dahl salt-sensitive (DS) rats were fed with normal diet (0.19% NaCl) or a high-salt diet (8% NaCl) from 7 weeks of age. Benidipine (4mg/kg) or vehicle (0.5% w/v methylcellulose 400cP) was administered orally after the start of the feeding. DS rats fed the high-salt diet showed an increase in systolic blood pressure (SBP), which was accompanied by the gain of heart weight. SBP was significantly lower in the benidipine group than in the vehicle group. The weight of heart was significantly decreased in the benidipine group.
Keywords: Diseased state and drug effect analysis

overall_design: Three samples were analyzed, the hearts of rat with normal diet (normal), high-salt diet plus vehicle (control), high-salt diet plus Benidipine (Benidipine). We use 2 arrays: control vs. normal and Benidipine vs. control. Replicates and dye swaps were not performed.

first: Kazuyo

last: Takaki

first: Norihiko

last: Shiraishi

first: Kazuhide

last: Hasegawa

first: Kozo

last: Yao

first: Toshio

last: Ota


title: Male and female Fundulus exposed to arsenic, and their parentally exposed offspring

status: Public on Jun 24 2009

city: Pendleton

first: Lisa

last: Bain

state: SC

address: P. O. Box 709

department: Biological Sciences

institute: Clemson University

platform_organism:
Fundulus heteroclitus
Pseudopleuronectes americanus


title: Effect of Dietary Grain on Rumen Papillae Gene Expression in Holstein Dairy Cows

status: Public on Aug 28 2009

city: Guelph

first: Michael

middle: Alexander

last: Steele

state: Ontario

address: 50 Stone Road East, Building #70

department: Animal and Poultry Science

country: Canada

institute: University of Guelph

summary: Four mature, non-lactating dairy cattle were transitioned from a high forage diet (HF; 0% grain) to a high grain diet (HG; 65% grain) that was fed for three weeks.  Rumen papillae biopsies were performed during the HF baseline (week 0) and after the first (week 1) and third week (week 3) of the grain challenge to create a transcript profile for the the short and long-term adaption of the rumen epithelium during ruminal acidosis.

overall_design: Comparison between three weekly means  (n=4 for each week, 12 arrays in total)

first: Brian

middle: W

last: McBride


title: Allele specific expression in Arabidopsis thaliana Col-0 x Van-0 F1 hybrids

status: Public on Aug 15 2009

city: Chicago

first: Justin

last: Borevitz

state: IL

department: Ecology and Evolution

institute: University of Chicago

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


title: Molecular profiling of breast cancer cell lines defines relevant tumor models

status: Public on Jul 10 2009

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University


title: Gene expression data in heifers with persistently infected (PI) or transiently infected (TI) fetuses.

status: Public on Jun 15 2009

city: Bozeman

first: Kate

last: McInnerney

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary: The response to the presence of the ncpBVDV-infected PI or TI fetus is expected to provide information on the impact of the PI fetus on the immune response of the dam

overall_design: Fetal PI infection was induced by intranasal inoculation of pregnant heifers with ncpBVDV on day 75 of gestation. Fetal transient infection (TI) was induced by infection of pregnant heifers with ncpBVDV on day 175 of gestation. Control heifers were kept uninfected. Blood samples from pregnant heifers of the PI and control groups were collected on day 160 of gestation. Blood samples of PI, TI and healthy fetus carrying heifers were collected for microarray on day 190 of gestation.

first: Smirnova

last: Natalia

first: Ptitsyn

last: Andrey

first: Austin

last: Kathleen

first: Bielefeldt-Ohmann

last: Helel

first: VanCampen

last: Hana

first: Han

last: Hyungchul

first: vanOlphen

last: Alberto

first: Hansen

last: Thomas


title: Using pooled earthworm RNA to test 244K probes on TA-1, TA-2, TA-3, TA-4 test arrays

status: Public on Jun 12 2009

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC


title: DNA packaging of Murine spermatozoal chromatin

status: Public on Jun 09 2009

city: Leeds

first: David

last: Miller

address: Clarendon Way

department: Leeds Institute for Genetics and Health Therapeutics

institute: Leeds University

summary: During mammalian spermiogenesis, the majority of the nucleosomes packaging the male haploid genome are replaced by protamines to produce a highly compact chromatin architecture that is critical to male fertility. We have carried out a genomewide survey of murine spermatozoal chromatin using a  micrococal nuclease approach to characterise the DNA sequences that remain packaged by histones.

overall_design: Limited digestion with micrococcal nuclease facilitates the release of a nucleosome-rich chromatin from mature spermatozoa. Whole genome CGH arrays were used to map the histone and protamine bound portions of spermatozoal DNA.

first: D

first: A

last: Arpanahi

first: M

last: Brinkworth

first: S

last: Krawetz

middle: E

last: Platts

last: Saida

first: P

last: Tedder

last: Iles


title: Muscle gene expression of lambs with maternal callipyge allele

status: Public on Jun 10 2009

city: West Lafayette

first: Christopher

last: Bidwell

state: IN

address: 125 South Russell Street

department: Animal Sciences

institute: Purdue University

summary:
Lambs that inherit a callipyge allele from their dam have an up-regulation of maternally imprinted transcripts near the callipyge mutation but do not exhibit muscle hypertrophy. It is not clear what effects these maternally expressed transcripts have in the muscle or how the inheritance of a maternal callipyge allele prevents the expression of the callipyge phenotype which is seen paternal heterozygotes only.
This experiment utilized bovine gene expression arrays to profile the gene expression of the semimembranosus muscle of 30 day old half-sibling lambs of all four possible genotypes with respect to the callipyge allele (+/+, C/+, +/C, and C/C).

Keywords: allele effect

overall_design:
10 lambs were used for this study. N=3 biological reps for C/C genotype, N=3 biological reps for Cmat/+ genotype, N=2 biological reps for +/Cpat genotype, and N=2 biological reps for +/+ genotype. Pairwise contrasts were performed to analyze the presence of a maternally inherited callipyge allele and the effect on a homozygous animal (+/C vs CC; +/+ vs C/+; and C/+ vs C/C).

These data make up two experiments.
[1] The maternal allele (4 genotype) experiment compares all four possible genotypes of a particular allele at one age and one tissue (30 days semimembranosus).
[2] The paternal allele (2 genotype) experiment compares only the NC and the NN genotypes in one tissue (SM) across 4 ages (10, 20, 30, and 80 days).

Images were interpreted with Microarray Suite version 5.0 (MAS5.0) in GCOS with no scaling or normalization (i.e., Samples GSM298143-GSM298164). Images were also interpreted by RMA using Bioconductor package of R (i.e., Samples GSM298165-GSM298186).

first: Jolena

middle: N

last: Fleming-Waddell

first: Gayla

last: Olbricht

first: Tasia

middle: M

last: Taxis

first: Tony

last: Vuocolo

first: Keren

last: Byrne

first: Bruce

last: Craig

first: Ross

middle: L

last: Tellam

first: Michael

last: Neary

first: Noelle

last: Cockett


title: Functional genomic analysis of frataxin deficiency, Agilent data

status: Public on Jun 02 2009

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary:
Functional genomic analysis of frataxin deficiency reveals tissue-specific alterations and identifies the PPARγ pathway as a therapeutic target in Friedreich's ataxia

Friedreich's ataxia (FRDA), the most common inherited ataxia, is characterized by focal neurodegeneration, diabetes mellitus, and life-threatening cardiomyopathy. Frataxin, which is significantly reduced in patients with this recessive disorder, is a mitochondrial iron-binding protein, but how its deficiency leads to neurodegeneration and metabolic derangements is not known. We performed microarray analysis of heart and skeletal muscle in a mouse model of frataxin deficiency, and found molecular evidence of increased lipogenesis in skeletal muscle, and alteration of fiber-type composition in heart, consistent with insulin resistance and cardiomyopathy, respectively. Since the peroxisome proliferator-activated receptor gamma (PPARγ) pathway is known to regulate both processes, we hypothesized that dysregulation of this pathway could play a key role in frataxin deficiency. We confirmed this by showing a coordinate dysregulation of the PPARγ coactivator Pgc1a and transcription factor Srebp1 in cellular and animal models of frataxin deficiency, and in cells from FRDA patients, who have marked insulin resistance. Finally, we show that genetic modulation of the PPARγ pathway affects frataxin levels in vitro, supporting PPARγ as a novel therapeutic target in FRDA.

overall_design: To compare frataxin deficient (KIKO) mice vs. WT, heart and skeletal muscle. Three replicates (KIKO vs WT), with dye swap

first: Daniele

last: Marmolino

first: Daning

last: Lu

first: Qing

last: Wang

first: Miriam

last: Cnop

first: Myriam

last: Rai

first: Fabio

last: Acquaviva

first: Sergio

last: Cocozza

first: Massimo

last: Pandolfo

first: Daniel

middle: H

last: Geschwind


title: Hybrid Poplar H11-11 Systemic Herbivory Response

status: Public on Jun 03 2009

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

institute: University of British Columbia


title: Distinctive Chromatin in Human Sperm Packages Genes that Guide Embryo Development: ChIP-chip

city: Salt Lake City

first: Bradley

middle: R.

last: Cairns

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: HHMI and Huntsman Cancer Institute

summary: As nucleosomes are widely replaced by protamine in mature human sperm, epigenetic   contributions to embryo development appear limited.  However, our genome-wide approaches find nucleosomes at low levels genome-wide, but also significantly enriched at imprinted gene clusters, miRNA clusters, HOX gene clusters, and the promoters of other developmental transcription and signaling factors. Developmental promoters were often DNA hypomethylated, and bore histone modifications localized to discrete locations: H3K4me2 is enriched at certain developmental promoters, whereas large blocks of H3K4me3 localize to a subset of developmental promoters, regions in HOX loci, certain non-coding RNAs, and generally to paternally-expressed imprinted loci.  In contrast, H3K4me3 is generally absent at paternally-repressed imprinted loci. Interestingly, repressive H3K27me3 is enriched at many developmental promoters that lack early expression in embryos, with significant overlap with bivalent (H3K4me3/H3K27me3) promoters in ES cells. Taken together, epigenetic marking in sperm is extensive, and correlated with developmental regulators.

overall_design:
*Use of ChIP-chip to identify regions enriched for methylated DNA, protamine, histone, and several histone variants in human sperm.

*Histone Localization: Chromatin was prepared from 40 million sperm as described previously (1) in the absence of crosslinking reagent, treated with sequential and increasing MNase (10U-160U), and centrifuged to sediment protamine-associated DNA, releasing mononucleosomes. The pooled mononucleosomes were gel purified (~140-155 bp) for sequencing and array analysis. Histone localization on arrays was performed using a single donor with 3 biological replicas and normalized to total genomic DNA (control).

*Chromatin IP and Preparation for Genomics Methods: ChIP methods were as described previously (2) but were performed without a cross linking agent and slight modifications to the salt levels, 250 mM NaCl, 200 mM LiCl, and replaced the TE wash with 150 mM PBS wash. ChIPs hybridized to arrays were performed from a single donor: H3K4me2 had 2 biological replicas, H3k4me3 had 3-replicas, TH2B had 2 replicas, and all the modifications data were normalized to the gel purified array monucleosomes.

*Methylation Profiling Using MeDIP: This procedure was described previously (3). Samples were hybridized to Agilent expanded promoter arrays, treated according to standard Agilent conditions, and scanned in an Agilent scanner. Sperm MeDIP had three replicas and Fibroblast had 2 replicas. Both Sperm and Fibroblast MeDIPs were normalized to their corresponding input fractions.

1. Zalenskaya, I.A., Bradbury, E.M. & Zalensky, A.O. Chromatin structure of telomere domain in human sperm. Biochem Biophys Res Commun 279, 213-8 (2000).
2. Gordon, M. et al. Genome-Wide Dynamics of SAPHIRE, an Essential Complex for Gene Activation and Chromatin Boundaries. Mol Cell Biol 27, 4058-69 (2007).
3. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39, 457-66 (2007).

The '*EnrichedRegions.xls' supplementary files list the enriched regions. See 'GSE15701_EnrichedRegions_README.txt'.

The '*OligoRatioData.zip' folders have the supplementary files containing oligo ratio data (log2(AveTreatment/AveControl)). See 'GSE15701_OligoRatioData_README.txt'.

first: S

middle: S

last: Hammoud

first: David

last: Nix

first: Haying

last: Zhang

first: Douglas

middle: T

last: Carrell


title: All Tumor Sector Experiments (T1-T20)

city: Cold Spring Harbor

first: Nicholas

last: Navin

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

overall_design:
ROMA CGH experiments were conducted on four to six dissected sectors (S1-S6) from single primary ductal carcinomas (T1-T20).  T1-T4 were analyzed by sectoring and analysis by ROMA.  T5-T20 were analyzed using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.

The genomic DNA from each tumor was labeled with Cy5 and a reference fibroblast genome was labeled with Cy3 and cohybridized to a ROMA microarray (85K or 390K). Experiments were performed in color-reversal by dye-swapping samples and hybridizing the labeled DNA to a second microarray for T1-T15 experiments, but not for T16-T20 experiments.


title: Transcriptome analysis of bovine mammary gland tissue treated with E. coli for 24 hours

status: Public on Jun 01 2009

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary:
By comparison of the transcriptome profiles of infected and healthy udder tissue we analyse gene expression in the late stage of infection with E. coli 1303.
Differentially expressed genes and transcription factors regulating coexpressed genes identified by SOTA clustering were used to identify key genes that define late stage of infection with E. coli 1303.

overall_design: 10 samples, two conditions: E. coli treated for 24h vs healthy control * five replicates

last: Mitterhuemer

first: A

last: Klanner

first: E

last: Wolf

first: H

last: Blum

first: W

last: Petzl

first: D

last: Mehne

last: Zerbe


title: Clostridium beijerinckii fermentation time course

city: Urbana

first: Zhen

last: Shi

address: 1206 West Gregory Drive

department: Institute for Genomic Biology

institute: University of Illinois

sample_organism:
Clostridium beijerinckii
Clostridium beijerinckii NCIMB 8052

overall_design: Refer to individual Series


title: E. coli infection induces distinct local and systemic transcriptome responses in the mammary gland


title: Transcriptome analysis of bovine mammary gland tissue of an udder quarter adjacent to an E.coli treated one for 24 hrs

summary:
By comparison of the transcriptome profiles of udder quarters neighboring to infected quarters and healthy udder tissue we analyse gene expression in the late stage of infection with E. coli 1303.
Differentially expressed genes and transcription factors regulating coexpressed genes identified by SOTA clustering were used to identify key genes that define systemic reactions to infection with E. coli 1303.

Keywords: disease state analysis

overall_design: 10 samples, two conditions: udder quarters neighboring to one which was treated with E. coli for 24h vs healthy control * five replicates

last: Klose

last: Petzlne


title: Transcriptome analysis of bovine mammary gland tissue treated with E. coli for 6 hours

summary:
By comparison of the transcriptome profiles of infected and healthy udder tissue we analyse gene expression in the early stage of infection with E. coli 1303.
Differentially expressed genes and transcription factors regulating coexpressed genes identified by SOTA clustering were used to identify key genes that define early stage of infection with E. coli 1303.

Keywords: disease state analysis

overall_design: 10 samples, two conditions: E. coli treated for 6h vs healthy control * five replicates


title: Symbiodinium clade content drives host transcriptome more than thermal stress in the coral Montastraea faveolata

status: Public on May 31 2009

city: San Francisco

first: Michael

last: DeSalvo

department: Department of Anesthesia

institute: UC San Francisco


title: Rat liver. Control vs. Chemical treated: time course

status: Public on Jun 23 2009

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

institute: Chemicals Evaluation and Research Institute, Japan


title: Quiescent keratinocytes and fibroblasts: radiation dose response

first: Philip

last: Moos

department: Pharmacology & Toxicology

institute: University of Utah

summary:
Skin is usually exposed during human exposures to ionizing radiation, however there are few experiments that evaluate the radiation responsiveness of the cells of the epidermis (keratinocytes) and those of the dermis (fibroblasts) in the same studies.  We evaluated the transcriptional responses of quiesent primary keratinocytes and fibroblasts from the same individual and compared them with quiescent keratinocytes and fibroblasts that were immortalized by human telomerase (hTert).
The primary transcriptional responses to 10-500 cGy ionizing radiation were p53-mediated responses; however, we did identify distinct responses between the keratinocytes and the fibroblasts.

Keywords: keratinocytes and fibroblasts - dose response to ionizing radiation

overall_design: Four cell types (primary keratinocytes, hTert immortalized keratinocytes, primary fibroblasts, hTert immortalized fibroblasts) grown to quiescence, treated with 0, 10, 100 or 500 cGy gamma irradiation, RNA collected at 4 hrs.

first: Raymond

last: Warters


title: Transcription Factor Promyelocytic Leukemia Zinc Finger Protein regulates Interferon Stimulated Gene expression

status: Public on May 22 2009

city: Clayton

first: Dakang

last: Xu

state: Victoria

address: 27-31 Wright St

department: Monash Institute of Medical Research

institute: Monash University

first: Michelle

last: Holko

first: Anthony

last: Sadler

first: B

last: Scott

last: Higashiyama

first: Windy

last: Berkofsky-Fessler

first: Melanie

last: McConnell

first: Pier

middle: P

last: Pandolfi

first: Jonathan

middle: D

last: Licht

first: Bryan

last: Williams


title: Insulator protein binding profiles and gene expression analysis of Drosophila melanogaster Kc and Mbn2 cell lines

status: Public on May 15 2009

city: Atlanta

first: Ashley

last: Bushey

state: GA

address: 1510 Clifton Rd. RRC 1071B

department: Biology

institute: Emory University


title: Hypothalamus transcriptome profile suggests an anorexia-cachexia syndrome in anx/anx mouse model

status: Public on May 11 2009

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

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

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

summary:
The anx/anx mouse displays poor appetite and lean appearance and is considered a good model for the study of anorexia nervosa. To identify new genes involved in feeding behavior and body weight regulation we performed an expression profiling in the hypothalamus of the anx/anx mice. Using commercial microarrays we detected 156 differentially expressed genes and validated 92 of those using TaqMan low-density arrays. Our results showed an enrichment of deregulated genes involved in cell death, cell morphology and cancer as well as an alteration of several signaling circuits involved in energy balance including neuropeptide Y and melanocortin signaling. The expression profile along with the phenotype let us to conclude that anx/anx mice resemble the anorexia-cachexia syndrome typically observed in cancer, infection with human immunodeficiency virus or chronic diseases rather than starvation, and that anx/anx mice could be considered a good model for the treatment and investigation of this condition.
Keywords: genetic mutation analysis

overall_design: Total RNA expression profile comparison between 3 pairs of anx/anx mice and wild type littermates in brain hypothalamus and neocortex

first: Josep

last: Mercader

first: Juanjo

last: Lozano

first: Mara

last: Dierssen

first: Joana

last: Visa

first: Mònica

last: Gratacòs

first: Xavier

last: Estivill


title: Smooth muscle cells in atherosclerosis-prone and resistant regions of the aorta of apoE-/- mice at age of 4 months

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: This study compared gene expression in smooth muscle cells (SMCs) in atherosclerosis-prone and atherosclerosis-resistant aorta segments in 4 months old apolipoprotein E-deficient (apoE-/-) mice before plaque development. In a parallel experiment, both regions were compared in young C57Bl/6 mice. Aortas of 3 male and 3 female ApoE-/- mice were isolated, perfused with triton X-100 to remove endothelial cells and divided in an atherosclerosis-prone region (AA: ascending aorta, aortic arch and proximal 2 mm of thoracic aorta) and a resistant region (TA: central thoracic aorta, i.e. 6 mm distal from the proximal 2 mm). Microarray analysis (VIB-MAF) of pooled total RNA showed differential expression (>2-fold difference) for 244 genes. Up- or downregulation in the AA was observed for 186 and 58 genes respectively. Differential expression of 6 genes was confirmed using real-time PCR. The 201 genes that showed exclusively differential expression in apoE-/- mice were related to processes involved in atherosclerosis, such as cell adhesion, proliferation, differentiation, motility and death, lipid metabolism and immune responses. Furthermore, the transcription profile of the AA was in accordance with a more synthetic SMC phenotype. These results point to an altered transcriptome in SMCs in the aorta of apoE-/- mice at the atherosclerosis-prone location before actual lesion development. This suggests that SMCs, in addition to endothelial cells, can facilitate plaque formation at predilection sites.

overall_design: samples were hyrbidized in dye-swap.

first: Tim

last: Van Assche

first: Jan

last: Hendrickx

first: Pieter-Jan

last: Guns

first: Wim

last: Martinet

first: Paul

last: Fransen

first: Hidde

last: Bult


title: Smooth muscle cells in atherosclerosis-prone and resistant regions of the aorta of C57Bl/6 mice at age of 4 months

summary: This study compared gene expression in smooth muscle cells (SMCs) in atherosclerosis-prone and atherosclerosis-resistant regions of the aorta of C57Bl/6 mice. In a parallel experiment, both regions were compared in young, plaque-free apolipoprotein E-deficient (apoE-/-) mice. Aortas of 3 male and 3 female C57Bl6 mice were isolated, perfused with triton X-100 to remove endothelial cells and divided in an atherosclerosis-prone region (AA: ascending aorta, aortic arch and proximal 2 mm of thoracic aorta) and an atherosclerosis-resistant region (TA: central thoracic aorta,i.e. 6 mm distal from the proximal 2mm of the thoracic aorta). Microarray analysis (VIB-MAF) of pooled total RNA showed differential expression (>2-fold difference) for 70 genes. Up- or downregulation in the AA was observed for 33 and 37 genes respectively. Differential expression of 3 genes (ATPase, Na+/K+ transporting, beta 1 polypeptide, sarcolipin and homeo box B7) was confirmed using real-time PCR. Twenty five genes showed exclusively differential expression in C57BL6 mice. Only 7 could be linked to specific processes: development (4) and cell growth (3). The other 18 genes were all involved in different processes. Among the 45 genes showing differential expression in C57Bl/6 as well as apoE-/- mice, most were related to development (13), cell growth (8) and transcription (10). These results point to an altered transcriptome in SMCs of the C57Bl/6 aorta at an atherosclerosis-prone location. This is in agreement with findings in endothelial cells in atherosclerosis-prone regions. It could be due to biomechanical differences, for instance in wall tension or shear stress, or the different embryological origin of SMCs in AA and TA.

overall_design: Samples were hybridized in dye-swap design.


title: Smooth muscle cells in atherosclerosis-prone and resistant regions of aorta


title: Effect of IL-1 alpha, TNF alpha, or IFN gamma on gene expression levels in thyroid follicles (Euthyroid Graves' Disease)

status: Public on Apr 28 2009

city: Shinjuku-ku

first: Kanji

last: Sato

state: Tokyo

address: Kawada-cho 8-1

department: Institute of Clinical Endocrinology

institute: Tokyo Women's Medical University

summary:
Graves’ disease is characterized by goiter, palpitation and exophthalmos (Merseburg’s trias). However, a few patients develop exophthalmos even though their thyroid function is normal, a condition known as euthyroid Graves’ disease (EGD). It remains unknown why these patients remain euthyroid, even though they have potent thyroid-stimulating antibody (TSAb).  To investigate whether the immunoglobulins (IgGs) obtained from EGD patients elicit thyroid hormone-releasing activity (THRA), thyroid follicles obtained from Graves’ patients were cultured in agarose-coated culture dishes, and 125I incorporated into the thyroid follicles and organic 125I (mainly de novo-synthesized 125I-T3+125I-T4) released into the culture medium by TSH or purified IgGs were determined as thyroid hormone-releasing activity (THRA). This thyroid follicle culture system allows maintenance of the Wolff-Chaikoff effect, and the expression of mRNA for the sodium-iodide symporter is decreased by high concentrations of iodide (10-6-10-4M) and therapeutic concentrations of amiodarone (1-2microM).  hTSH elicited THRA most efficiently at 0.4-10 microU/ml, suggesting that thyroid function is controlled within the normal range of TSH concentration (0.4-4.0 microU/ml). All IgGs obtained from hyperthyroid Graves’ patients elicited THRA equivalent to more than 4.6 microU/ml hTSH. IgGs obtained from EGD patients also had potent THRA, whereas IgGs obtained from normal subjects and Graves’ patients in complete remission had no significant THRA.    When thyroid follicles from Graves’ thyroid, into which a number of lymphocytes had infiltrated, were used, only slight THRA was elicited by bTSH or Graves’ IgGs, probably due to inflammatory cytokines produced by immunocompetent cells that could not be separated during gentle centrifugation. Indeed, when thyroid follicles were cultured with autologous intrathyroidal lymphocytes, interleukin-2 completely abolished TSH-induced THRA.   When thyroid follicles were cultured with inflammatory cytokines (interleukin-1, tumor-necrosis factor-alpha, or interferon-gamma), each cytokine inhibited TSH-induced THRA in a concentration-dependent manner. These cytokines at lower concentrations synergistically and completely inhibited TSH-induced THRA. Microarray analyses of thyroid follicles cultured with IL-1alpha, TNF-alpha, or INF-gamma revealed decreased expression of mRNAs for TSHR, NIS, TPO and thyroglobulin, accompanied by increased expression of mRNAs for chemokines and cytokines.   These findings suggest that IgGs obtained from patients with EGD have potent THRA in vitro, whereas in vivo, these IgGs are unable to elicit biological activity in the thyroid gland. Presumably, immunocompetent cells that infiltrate the thyroid gland produce inflammatory cytokines that synergistically inhibit thyroid function. Since a similar phenomenon may occur in the retroorbital tissues, these patients may develop exophthalmos despite having a normal serum level of TSH.
This data will be published in Hyperthyroidism: Etiology, Diagnosis and Treatment (editor-in-chief;Dr.Frank Clumbus,Nova Science Publishers, Inc, New York, USA)

overall_design: One conditioned experiments: control vs. IL-1 alpha 5ng/ml, cultured for 24 hours; control vs. TNF alpha 20ng/ml, cultured for 24 hours; control vs. IFN gamma 1000U/ml, cultured for 48 hours.

first: Kazuko

last: Yamazaki


title: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection

first: Robert

last: Lucito

department: Genome Center