title: Differentiating size-dependent responses of juvenile pink salmon (Oncorhynchus gorbuscha) to sea lice (Lepeophtheirus salmonis) infections

status: Public on Feb 26 2011

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

summary: Salmon infected with an ectoparasitic marine copepod, the salmon louse Lepeophtheirus salmonis, incur a wide variety of consequences depending upon host sensitivity. Juvenile pink salmon (Oncorhynchus gorbuscha) migrate from natal freshwater systems to the ocean at a young age relative to other Pacific salmon, and require rapid development of appropriate defences against marine pathogens. We analyzed the early transcriptomic responses of naïve juvenile pink salmon of sizes 0.3g (no scales), 0.7g (mid-scale development) and 2.4g (scales fully developed) to a low-level laboratory exposure with early moult stage L. salmonis. All infected size groups exhibited unique transcriptional profiles. Inflammation and inhibition of cell proliferation was identified in the smallest size class (0.3g), while increased glucose absorption and retention was identified in the middle size class (0.7g). Tissue-remodelling genes were also up-regulated in both the 0.3g and 0.7g size groups. Profiles of the 2.4g size class indicated cell-mediated immunity and possibly parasite-induced growth augmentation. Understanding a size-based threshold of resistance to L. salmonis is important for fisheries management. This work characterizes molecular responses reflecting the gradual development of innate immunity to L. salmonis between the susceptible (0.3g) and refractory (2.4g) pink salmon size classes.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Six-condition experiment, 3 size groups each infected and uninfected, duplicate tanks. Biological replicates: 6 control, 6 infected for each size group. Sampled 6 days post exposure. cDNA samples with reference design (aRNA), two-color array.

middle: J

last: Sutherland

first: Stuart

last: Jantzen

first: Dan

middle: S

first: Simon

last: Jones


title: Methylation profile in breast cancer

status: Public on Feb 23 2011

city: Daejeon

first: Myung Soon

last: Kim

address: Yeusung-gu

department: R&D

country: South Korea

institute: Genomictree

type: Methylation profiling by genome tiling array

summary: Agilent CpG microarray in combination with enriched methylated DNA by a MBD protein were carried out in each pool of genomic DNA from primary breast tumor and matched adjacent normal tissues.

overall_design:
1.Common reference vs enriched methylated DNA in tumor
2. Common reference vs enriched methylated DNA in adjacent normal
3. Then compare two data indirectly


title: Rice NSF45K microarray experiment to explain Xa21, NH1 and NRR mediated defense responses in rice

status: Public on Feb 28 2011

city: Yongin

first: Ki-hong

last: Jung

address: 1 Seocheon-dong

department: Plant Molecular Systems Biotechnology

institute: Kyung Hee University

summary:
Rice Xa21 resistance gene, which encodes a protein with predicted leucine-rich repeat (LRR), transmembrane, juxtamembrane, and intracellular kinase domains, conferred immunity to diverse strains of Xanthomonas oryzae pv. oryzae (Xoo). We generated Xa21 plant on TP309 background (Oryza Sativa Japonica). Systemic Acquired Resistance (SAR) in plants confers durable broad-spectrum resistance to pathogens and requires a phytohormone, salicylic acid (SA). Arabidopsis NPR1/NIM1 is a key regulator of the SAR response. Recently, we found that rice NPR1 homolog 1 (NH1) mediated enhanced resistance responses for Xoo (Chern et al., 2005b). We further investigated relating pathways in rice by identifying proteins that interact with NH1. One of them, constitutive over-expression of NH1 mediated negative regulator of resistance (NRR) gene caused enhanced susceptibility to Xoo , indicating that this gene product negatively affects to basal resistance response (Chern et al., 2005a). To dissect defense responses for rice bacterial blight pathogen, we planed microarray using two resistant mutant named with Xa21-TP309, NH1ox and one super-susceptible mutant (NRRox) before pathogen inoculation and one day post pathogen inoculation.

Keywords: Biotic stress response

overall_design: Two or Three-condition experiment, NH1ox vs wild type control (LG) at two durations of Xoo inoculation (0d and 1d); NRRox vs wild type control (LG) at two durations of Xoo inoculation (0d and 1d); and Xa21vs wild type control (TP309) at three durations of Xoo inoculation (0d,1d and 2d);. Biological replicates: 2 or 4, independently grown and harvested.

first: Pamela

last: Ronald

first: Peijian

last: Cao

first: Young-Su

last: Seo

first: Patrick

last: Canals

first: Laura

last: Bartley


title: Expression profiling of S. pyogenes in response to Glucose and mutation of the regulators CcpA and LacD.1

status: Public on Feb 27 2011

city: St. Louis

first: Colin

middle: Christopher

last: Kietzman

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology and Microbial Pathogenesis

country: USA

institute: Washington University in St. Louis

summary: Transcriptome changes were measured in S. pyogenes strain HSC5 in response to glucose availability, taking samples from the wild type strain (HSC5) grown in carbohydrate poor medium (C medium) versus this same medium with 1% (w/v) Glucose added. Furthermore, the effects of deletion of glucose responsive regulators CcpA and LacD.1 were measured by using isogenic mutants in these genes (Delta CcpA and Delta LacD.1 respectively) compared to the wild type parent strain (HSC5), both grown in C medium with 1% glucose.

overall_design: Experiments were carried out using two biological replicates for each variable tested (ie two independent RNA samples gathered on separate days),  and dye exchange experiments for each RNA sample tested were carried out.

middle: C

first: Michael

middle: G

last: Caparon


title: ERalpha ChIP-chip from HeLA-ER cells treated with E2

status: Public on Feb 22 2011

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary: We are studying the mechanisms by which the estrogen receptor, ERalpha, is recruited to and regulates genes with a non-direct DNA binding.  We performed ChIP-chip for ERalpha in E2 treated HeLa-ER cells, and looked at 19000 RefSeq genes to determine binding patterns of the receptor at promoters.  The experiment was performed in duplicate.

overall_design: ChIP-chip biological replicates for Eralpha in E2 treated HeLa-ER cells are included.

first: Heldring

last: Nina

first: Lee


title: SNP genotyping of cryptic complexity in structural chromosome abnormalities previously detected by cytogenetic analysis

city: Baltimore

first: Jonathan

last: Pevsner

state: MD

address: 707 N. Broadway

institute: Kennedy Krieger Institute

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

summary: Purpose: The purpose of this study was to evaluate SNP genotyping methodology as a means to detect chromosomal abnormalities previously diagnosed by G-band karyotype or fluorescence in situ hybridization (FISH) analysis and to determine the frequency of sub-microscopic (cryptic) chromosomal alterations in these subjects. Methods: We used the Illumina HumanHap Beadchip platform to genotype 40 individuals having previously detected chromosomal anomalies (by G-banded and/or FISH analysis). The resulting data were analyzed for signal intensity (log R ratio) and allelic composition (B allele frequency). Results: SNP array analysis detected 100% of previously identified cytogenetic abnormalities. Changes or clarifications of the ISCN karyotype designation assigned by conventional cytogenetic and/or FISH analysis were made in 82 % of the cases (32 of 39). Nine of the 39 cases (23%) involved a reassignment of an abnormal band while an additional 9 of the 39 (23%) resulted in a clarification of a sub-band assignment. In 8 more of the 39 cases (21%) the previously reported alterations were confirmed, however the SNP analysis also identified related cryptic alterations. SNP analysis not only confirmed FISH-detected abnormalities but also more precisely mapped the breakpoints of 6/6 patients. Investigations into the origin of de novo abnormalities in 15 trio families established that 12 /15 occurred on the paternal chromosome. Conclusions: SNP genotyping array analysis, confirmed all previously detected structural chromosomal abnormalities and provided additional, clinically-relevant genomic information in 82% of these alterations.

overall_design: To evaluate potential chromosomal abnormalities in patients, we measured SNPs using Illumina 550K and 300K arrays. In some cases we also measured SNPs in parents to determine whether deletions or duplications occurred de novo or were inherited.

first: Elizabeth

last: Wohler


title: Genome-wide expression profile analysis of the Candida glabrata Pdr1 regulon

status: Public on Feb 21 2011

city: Memphis

first: Katherine

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

summary: The ABC-transporters CgCdr1, CgPdh1, and CgSnq2 are known to mediate azole resistance in the pathogenic fungus Candida glabrata. Activating mutations in CgPDR1, a zinc cluster transcription factor, result in constitutive up-regulation of these ABC-transporter genes but to varying degrees. We examined the genome-wide gene expression profiles of two matched azole-susceptible and –resistant C. glabrata clinical isolate pairs. Of all the genes identified in the gene expression profiles for these two matched pairs, there were 28 genes that were commonly up-regulated with CgCDR1 in both isolate sets including YOR1, LCB5, RTA1, POG1, HFD1, and several members of the FLO gene family of flocculation genes. We then sequenced CgPDR1 from each susceptible and resistant isolate and found two novel activating mutations that conferred increased resistance when expressed in a common background strain in which CgPDR1 had been disrupted.  Microarray analysis comparing these re-engineered strains to their respective parent strains identified a set of commonly differentially-expressed genes, including CgCDR1, YOR1, and YIM1, as well as genes uniquely regulated by specific mutations. Our results demonstrate that while CgPdr1 activates a broad repertoire of genes, specific activating mutations result in the activation of discrete subsets of this repertoire.

overall_design:
We examined the genome-wide gene expression profiles of two matched azole-susceptible and –resistant C. glabrata clinical isolate pairs to determine the core regulon of CgPDR1 as well as how different activating alleles of PDR1 can affect the differential expression of target genes.
genotype: wildtype allele: SM1, 6856, SM1Dpdr1/PDR1-SM1, SM1Dpdr1/PDR1-6856
genotype: activating allele: SM3, 6955, SM1Dpdr1/PDR1-SM3, SM1Dpdr1/PDR1-6955

first: Kelly

middle: E

last: Caudle

first: Nathan

middle: P

last: Wiederhold

first: Lijing

last: Xu

first: Ramin

last: Homayouni

first: P

middle: D

last: Rogers


title: The Kinase SGK1 in the Endoderm and Mesoderm Promotes Ectodermal Survival by Downregulating Components of the Death-Inducing Signaling Complex

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

summary: A balance between cell survival and apoptosis is essential for animal development. Although proper development involves multiple interactions between germ layers, little is known about the intercellular and intertissue signaling pathways that promote cell survival in neighboring or distant germ layers . We show that serum- and glucocorticoid-inducible kinase 1 (SGK1) promoted ectodermal cell survival during early Xenopus embryogenesis through a non-cell-autonomous mechanism. Dorsal depletion of SGK1 in Xenopus embryos resulted in shortened axes and reduced head structures with defective eyes, and ventral depletion led to defective tail morphologies. Although the gene encoding SGK1 was mainly expressed in the endoderm and dorsal mesoderm, knockdown of SGK1 caused excessive apoptosis in the ectoderm. SGK1-depleted ectodermal explants showed little or no apoptosis, suggesting non-cell-autonomous effects of SGK1 on ectodermal cells. Microarray analysis revealed that SGK1 knockdown increased the expression of genes encoding FADD and caspase-10, components of the death-inducing signaling complex (DISC). Inhibition of DISC function suppressed excessive apoptosis in SGK1-knockdown embryos. SGK1 acted through the transcription factor nuclear factor kappaB to stimulate production of bone morphogenetic protein 7 (BMP7), and overexpression of BMP7 in SGK1-knockdown embryos reduced the abundance of DISC components. We show that phosphoinositide 3-kinase (PI3K) functioned upstream of SGK1, thus revealing an endodermal and mesodermal pathway from PI3K to SGK1 to NF-kappaB that produces BMP7, which provides a survival signal to the ectoderm by decreasing DISC function.

overall_design:
To identify genes whose expression levels are regulated by SGK1 in Xenopus development, we performed genome-wide analysis by using Affymetrix GeneChip oligonucleotide microarrays.
We performed two independent experiments. For each microarray experiment, we radially injected control-morpholino or xSGK1-morpholinos into 4-cell embryos, cultured the embryos until stage 12, extracted total RNAs using Trizol (Invitrogen) and purified them on RNeasy columns (Qiagen). Synthesis of cDNA, in vitro transcription and biotin labeling of cRNA, and hybridization to the Xenopus laevis genome array (Affymetrix) were performed according to the Affymetrix protocol (Two-Cycle Target Labeling Assays). Hybridized arrays were scanned using an Affymetrix GeneChip Scanner. Scanned chip images were analyzed with GeneChip Operating Software (GCOS) v. 1.4.

first: Tatsuya

last: Endo

first: Morioh

last: Kusakabe

first: Kazunori

last: Sunadome

first: Takuya

last: Yamamoto


title: miRNA profiling from T-ALL cells

status: Public on Feb 19 2011

city: Boston

first: Xiaoyu

last: Li

state: MA

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

summary: The NOTCH1 signaling pathway is a critical determinant of cell fate decisions and drives oncogenesis through mechanisms that are incompletely understood. To elucidate tumorigenic pathways that cooperate with activated Notch1 in leukemogenesis,we performed miRNA expression profiling of normal CD4+CD8+ thymocytes, non-malignant ICN1 over-expressing CD4+CD8+ cells and ICN1-induced tumor CD4+CD8+ cells.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Three groups of the murine T cells: Control CD4+CD8+ normal thymocytes vs.non-malignant ICN1-expressing CD4+CD8+ cells vs. ICN1-tumor CD4+CD8+ cells .

first: Harald

last: von Boehmer


title: Expression data of Arabidopsis wild type Col and mutant pcfs4-1

city: Oxford

first: Quinn

state: OH

address: 316, Person Hall, High Str.

department: Botany

institute: Miami University

type: Expression profiling by genome tiling array

summary:
Arabidopsis polyadenylation factor PCFS4 functioned in the alternative polyadenylation of FCA. To identify additional genes differetially processed by PCFS4, we compared the transcriptomes of PCFS4 mutant, pcfs4-1 and wild type Col with  Arabidopsis tiling array analyses and a newly developed data processing protocol, RADPRE.
We found 68 genes were differentially processed and 114 genes differetially expressed in pcfs4-1 mutant. The top 7 of 68 differetially processed genes were further confirmed with real-time RT-PCR analysis.

overall_design: Arabidopsis plants were grown in a radomized block design with 3 replicates for each of pcfs4-1 and Col. Each block contained one pcfs4-1 and one Col. above ground tissue of 15-day old seedlings was collected 8 hours after dawn. Total RNAs were extracted using Concert Plant RNA reagent (Invitrogen); The double-stranded cDNA targets prepared from total RNA were labeled and hybridized to the Arabidopsis Tiling 1.0R array.

first: Qingshun

middle: Q

first: Denghui

last: Xing


title: Analysis of gene expression profiles after UVB irradiation in human keratinocytes

status: Public on Feb 17 2011

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
Dr. Liu's research group is interested in studying the expression and functions of galectin-3, -7 and -12, in particular the roles of these proteins in inflammation and neoplasm.
Members of the galectin family are known to participate in cellular homeostasis by modulating cell growth, controlling cell cycle progression, and inducing or inhibiting apoptosis. It is known that some galectins have similar functions. However, it is not fully understood whether they work cooperatively or not. As the outermost barrier of the body, skin is directly and frequently exposed to a prooxidative environment, including solar ultraviolet A (UVA), ultraviolet B (UVB) radiation, and air pollution. Several reports have shown that exposure of cells to UV increase or decrease the levels of galectins. For example, the amounts of galectin-7 mRNA and protein are increased rapidly after UVB irradiation of keratinocytes (Proc. Natl. Acad. Sci. USA 1999; 96:11329-34). Heat shock and subculturing decrease, while alkylating agents and UV-light increase galectin-3 (Cell Physiol Biochem 2000; 10:149-58). To analyze the change of all galectin gene expression profiles after UVB irradiation and to determine the presence or absence of coordinate regulation, we analyzed the gene expression profiles of keratinocytes exposed to UVB. Normal human epidermal keratinocytes (NHEK) were irradiated with 200 J/m2 of UVB. Total RNA will be extracted at 0, 6, 12 and 24 h after irradiation (duplicate) for analysis on the Glyco gene chip.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Several reports have shown that exposure to UV light can regulate levels of galectin in skin. This study seeks to analyze the changes in all galectin gene expression profiles post-UVB irradiation to determine the presence or absence of coordinate regulation. In this study, normal human keratinocytes were irradiated with 200J/m2 of UVB. Total RNA was extracted at 0, 6, 12, and 24-hour post irradiation time points, in duplicate. Samples were hybridized and analyzed using the GLYCOv2 array.

first: Fu-Tong

last: Liu

middle: R


title: Defining the Myb Transcriptional Program Controlled by via Genome-wide Chromatin Occupancy and Expression Analyses

city: Brisbane

first: paul

middle: james

last: LEO

state: Queensland

address: Princess Alexandria Hospital, Level 4 R-wing

country: Australia

institute: UQ Diamantina Institute  for cancer, Immunology and Metabolic Medicine

summary: We used the ERMYB cell line (Hogg et al., Oncogene 15, p2885-2898, 1997) as our model system to identify genes regulated by Myb using whole genome microarray expression profiling. ERMYB is a myeloid progenitor cell line derived by transformation of primary cells by an activated form of Myb (CT3-Myb) fused to the ligand binding domain of ERα. In these cells, activation of the ER-Myb fusion protein by estrogen is required to maintain a proliferative progenitor-like phenotype. The cells undergo monocytic differentiation when Myb is inactivated by withdrawal of β-estradiol (β-E2). However, re-induction of Myb within 24 hours can almost fully reverse the differentiation process. This feature enabled us to employ a novel kinetic expression profiling strategy, in that we withdrew β-E2 to inactivate Myb for 24 h, then re-added it for another 6 h  and monitored the gene expression across this time course. We reasoned that this strategy may be more likely to identify true Myb target genes than conventional approaches in which differential expression is examined only at the endpoint of induction. To exclude genes that might be responsive to ERα and not Myb we used the parent CT3-Myb cell line and measured the expression changes 6hrs after β-E2 withdraw and excluded those few gene that were differentially expressed.

overall_design: Triplicate total RNA samples from ERMYB cells were collected at 0, 6, and 24 hr after β-E2 withdrawal and 6 hr after β-E2 re-addition. Samples were analyzed by Illumina Mouse Whole Genome arrays (WG6). Probe intensities were variance stabilised and normalized by the Lumi package (Du et al., 2008). Differentially expressed genes were identified by the LIMMA package (Smyth, 2004) and then grouped into different classes according to their kinetic profiles.

first: Liang

last: Zhao

first: Evgeny

last: Glazov

first: Diwakar

last: Pattabiraman

first: Faisal

last: Al-Owaidi

first: Ping

last: Zhang

first: Matthew

middle: A

last: Brown

first: Paul

last: Leo

first: Thomas

last: Gonda


title: Gene expression in experimentally injured and control mouse spinal cords

summary: This laboratory works on selectins and their carbohydrate ligands in lymphocyte homing and inflammation. The lab also studies heparin-degrading endosulfatases and their roles in regulating the interactions of growth factors and morphogens with proteoglycans.

overall_design:
The purpose of the experiment is to examine gene expression profiles in spinal cords of injured as a function of time after a contusion injury. The tissue will be generated in the lab of Linda Noble, Professor in the Department of Neurological Surgery at UCSF who is an expert on the pathogenesis of spinal cord injury. Wild-type male C57B/6 mice (8-10 weeks of age) were used. Injuries were produced by contusion.
Spinal cords from control mice (uninjured) and experimental (injured) mice were processed (4 and 7 days after injury). A 3 mm length of spinal cord (centered at the injury) and a 3 mm segment from a distant site were isolated from each animal. Tissue from 3 mice were pooled for each sample. Three replicate samples per treatment group were processed for RNA. Thus, a total of 18 RNA samples were hybridized to 18 gene chips. The analysis will determine whether specific glycosylation changes accompany spinal cord injury. Of particular interest are changes in the sulfation profile of proteoglycan GAG chains (e.g., chondroitin sulfate) and in the appearance of potential carbohydrate ligands for infiltrating leukocytes bearing L-selectin or other endogenous lectins.

last: Rosen


title: ADAM13 knockdown in Xenopus laevis cranial neural crest

city: Amherst

first: Dominique

last: Alfandari

address: 661 North pleasant street

department: Vet & Animal Sciences

institute: University of Massachusetts

summary: ADAMs are transmembrane metalloproteases that control cell behavior by cleaving both cell adhesion and signaling molecules. The cytoplasmic domain of ADAMs can regulate the proteolytic activity by controlling the subcellular localization and/or the activation of the protease domain. Here we show that the cytoplasmic domain of ADAM13 is cleaved and translocates into the nucleus. Preventing this translocation renders the protein incapable of promoting cranial neural crest (CNC) cell migration in vivo, without affecting its proteolytic activity. In addition, the cytoplasmic domain of ADAM13 regulates the expression of multiple genes in the CNC. This study shows that the cytoplasmic domain of ADAM metalloproteases can perform essential functions in the nucleus of cells and may contribute substantially to the overall function of the protein.

overall_design:
Total RNA from cranial neural crest explants dissected from Xenopus laevis embryos at stage 15 to 17. Embryos were injected with either control morpholino (CMO), morpholino to ADAM13 (MO13) or MO13 and a fusion between GFP- and the cytoplasmic domain of ADAM13 (GFP-C13). Triplicate microarray correspond to independent experiments labeled DA4, DA5 and DA2. For each sample 1 is CMO, sample 2 is MO13 and sample 3 is MO13+C13. Embryos were injected with 10 ng of morpholino and 0.5 ng of GFP-C13 mRNA.

Supplementary files:
[1] matrix2_sig-genes.txt
CNC array: Genes significantly affected by the loss of ADAM13 p<0.01.
Normalized probe set generated by GC-RMA.
[2] matrix3_sig-genes.txt
CNC array: Genes significantly affected by the loss of ADAM13 and the addition of GFP-C13 p<0.01.
Normalized probe set generated by GC-RMA.

first: Helene

last: Cousin

first: Alban

last: Gaultier


title: Changes in gene expression during the transition from inflammation to cancer following Helicobacter felis infection

summary: We are now trying to elucidate the mechanism of Helicobacter-induced gastritis and gastric cancer. To identify genes involved in these Helicobacter-associated diseases, we infected Helicobacter felis to INS-GAS (insulin-gastrin transgenic) mice (C57BL/6 background) which shows accelerated development of gastritis and gastric cancer.

overall_design:
Three infected mice and three uninfected control mice (6 in total) were sacrificed periodically (2, 4, 6, 8 months after the infection), and total RNA was isolated from each stomach. These samples are subjected to gene microarray analysis.
Samples were obtained from mouse stomachs at 2, 4, 6, and 8/9 month post infection intervals. Control time points were taken at 0, 2, 4, 6, and 8 months. All samples, 22 in total, were hybridized to the GLYCOv2 array.

first: Minoru

last: Fukuda


title: Arthritis pathogenesis: Development of novel diagnostic and therapeutic approaches

summary: Chondrocytes are the only cell type in cartilage and play a pivotal role in tissue homeostasis and cartilage remodeling in Osteoarthritis (OA). OA-dependent metabolic changes affecting extracelluar matrix composition as well as variations in the response to cytokines and growth factors have been investigated in human chondrocytes. However, the molecular mechanisms causing age-dependent variation of the chondrocyte phenotype are poorly characterized. The proinflammatory mediator nitric oxide (NO) is produced when chondrocytes are exposed to cytokines such as IL-1. NO affects the energy metabolism of cells through interfering with mitochondrial respiration and glycolysis and has been implicated in extracellular matrix synthesis and degradation and chondrocyte death. NO may contribute to the aging process by compromising the energy balance in chondrocytes through the generation of an oxidizing environment and this may in turn affect matrix gene expression. In human chondrocytes NO effects on the expression of extacelluar matrix genes or genes related to matrix structure have not been addressed comprehensively.

overall_design: In this study cultured chondrocytes from a single donor was either be left unstimulated (control) or stimulated with IL-1, L-NMMA or IL-1 L-NMMA for a period of 8 days in order to achieve sufficiently high levels of intracellular NO and stable expression of a subset of genes. Samples were hybridized and analyzed using the GLYCOv2 array. L-NMMA (NG-monomethyl-L-arginine)  is a competitive inhibitor NO synthesis.

first: Martin

last: Lotz


title: Gallus gallus Control Versus SU5402, LY294002 or U0126 Treated Preingression Epiblast from Gastrula Stage Embryos

status: Public on Feb 20 2011

city: Tucson

first: Parker

middle: B

last: Antin

state: AZ

address: 1656 E. Mabel Street

department: Cell Biology and Anatomy

institute: University of Arizona

summary:
Transcriptional profiling of the preingression epiblast versus lateral epiblast, of preingression epiblast from control  embryos treated with the DMSO carrier vehicle (0.5%) versus embryos treated with SU5402, U0126 or LY294002.   Embryos were stages 5-6 at time of tissue isolation.  The preingression epiblast (E2 region) is the region of epiblast just lateral to the primitive streak. Lateral epiblast is the E3 region.
Two condition experiment. Samples for each condition isolated from at least 30 embryos.

overall_design: The experiments used isolated preingression epiblast, which is defined as the region of epiblast adjacent to the primitive streak that will ingress through the primitive streak.  Preingression epiblast was isolated by microdissection using tungsten needles from control embryos or embryos treated with SU5402, U0126 or LY294002.


title: Impact of mediator nitric oxide on gene expression in human chondrocytes

first: Steven

last: Head

summary:
Osteoarthritis (OA) is an aging-associated disease of diarthrodial joints that involves changes in the bone, cartilage and soft tissue. Chondrocytes are the only cell type in cartilage and play a pivotal role in tissue homeostasis and cartilage remodeling in OA. Age- or OA-dependent metabolic changes affecting extracelluar matrix composition as well as variations in the response to cytokines and growth factors have been investigated in human chondrocytes. However, the molecular mechanisms causing age-dependent variation of the chondrocyte phenotype are poorly characterized. The proinflammatory mediator nitric oxide (NO) is produced when chondrocytes are exposed to cytokines such as IL-1. NO affects the energy metabolism of cells through interfering with mitochondrial respiration and glycolysis and has been implicated in extracellular matrix synthesis and degradation and chondrocyte death. NO may contribute to the aging process by compromising the energy balance ! in chondrocytes through the generation of an oxidizing environment and this may in turn affect matrix gene expression. In human chondrocytes NO effects on the expression of extacelluar matrix genes or genes related to matrix structure have not been addressed comprehensively.
In chondrocytes NO has profound effects on extracellular matrix: Interleukin-1 induced the production of nitric oxide in human articular chondrocytes in alginate culture and simultaneously inhibited the biosynthesis of proteoglycans. NG-monomethyl-L-arginine (L-NMMA) inhibited nitric oxide formation and the suppression of proteoglycan synthesis. The nitric oxide donor, S-nitrosyl-acetyl-D,L- penicillamine (SNAP) also inhibited proteoglycan biosynthesis suggesting that interleukin-1 suppresses matrix synthesis through mechanisms involving the production of NO. Slices of rabbit articular cartilage synthesized large quantities of nitric oxide (NO) following exposure to IL-1 and strongly suppressed the incorporation of 35SO4 into the glycosaminoglycans (GAGs) of cartilage proteoglycans. Simultaneous treatment of cartilage fragments with IL-1 and L-NMMA inhibited NO synthesis in response to IL-1 and restored proteoglycan synthesis. SNAP reversibly mimicked the effect! of IL-1 on proteoglycan synthesis. These data suggest that endogenously synthesized NO is the mediator which reduces cartilage proteoglycan synthesis in response to cytokines such as IL-1. Aggrecan and type II collagen synthesis are also affected by NO. Our hypothesis entails that in human chondrocytes endogenous NO modulates the expression of matrix genes as well as enzymes involved in extracellular matrix remodelling.                         Experimental approach: In this experiment cultured chondrocytes from 3 donors was left unstimulated (control) or stimulated with IL-1, L-NMMA or IL-1 + L-NMMA for a period of 8 days in order to achieve sufficiently high levels of intracellular NO and stable expression of a subset of genes. Total RNA was isolated using the Trizol procedure. Gene expression will be probed using the Glycov2 chip.

overall_design: In this study cultured chondrocytes from three donors will either be left unstimulated (control) or stimulated with IL-1, L-NMMA or IL-1 L-NMMA for a period of 8 days in order to achieve sufficiently high levels of intracellular NO and stable expression of a subset of genes. 12 Samples were hybridized and analyzed using the GLYCOv2 array, three from each class.


title: Effect of GnRH on miRNA expression in LbetaT2 cells

status: Public on Feb 18 2011

first: Nick

last: Webster

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

summary: Mouse immortalized LbetaT2 gonadotrope cells treated with 100 nM GnRH for 2 h.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: GnRH treated LbetaT2 cells vs. untreated to assess whether GnRH regulates miRNA expression acutely.  Treated and untreated RNA labeled independently then hybridized together to 2-color array.  Duplicate arrays run with RNA from independent experiments.


title: Glycogene expression changes between different passages in the 4T1 Mouse metastatic breast cancer cell line

summary:
This laboratory's focus is on the immune response to carbohydrate antigens, with an emphasis on modalities to analyze and to increase the immune response. We are also interested in carbohydrate drug targeting.
The hypothesis is that these 2 variants have different cell surface carbohydrate expression, which results in different adhesion patterns, which ultimately results in different metastasis patterns. Evidence for expression differences and loss of the variants ability to metastasize to the lung could have clinical implications in the prevention of metastasis to different organs.

overall_design: The 4T1 mouse metastatic breast cancer cell line is known to change with passages in culture. Our data has shown changes cause the cells to metastasize to the intestine rather than to the lung. Four classes of RNA were analyzed: one each from 4T1 metastatic cell line variant #1, 4T1 variant #2, non-metastatic cell lines 4T07, and non-metastatic cell line 67NR. Classes were prepared in triplicate for a total of 12 samples. All samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.

first: Kate

last: Rittenhouse-Olson


title: Gene Expression patterns in mouse B16-OVA melanoma tumors

summary:
This laboratory focuses on selectin mediated recruitment during adoptive immunotherapy for metastatic cancer.
This study seeks to determine changes in the expression levels of Fucosyltransferases, Selectins, and cytokines in normal and inflamed mouse skin, melanoma tumor tissue of different sizes, and tumor cells grown in culture. Since the ability to treat the tumor effectively is directly related to the size of the tumor, differences in glyco-expression patterns may be of interest. In this study, five groups were hybridized and analyzed using the GLYCOv2 array.

overall_design: Each group was analyzed in triplicate. The groups were: Normal mouse skin, normal mouse skin inflamed by treatment with Oxazolone, B16-OVA melanoma tissue from 6 day tumors, B16-OVA melanoma tissue from 11 day tumors, and B16-OVA grown in cell culture.

first: Lloyd

last: Stoolman


title: Cell lines LS180 vs U937

summary: Dr. Esko's laboratory focuses on the structure, function, and biosynthesis of glycoproteins and proteoglycans. This laboratory also works on the design and synthesis of small molecule inhibitors of glycosylation.

overall_design: We analyzed the expression patterns of glycosyltransferase, growth factors, and receptors in endothelial cells derived from NDST1 deficient and wild-type mice using cancer cell line types U937 and LS180 .

first: Jeffrey

last: Esko


title: Normal vs Testoterone treated thymocytes

summary: This laboratory is focusing on to clarify the biologic relevance of a virulence factor known as trans-sialidase from Trypanosoma cruzi, the agent of the Chagas disease (American trypanosomiasis).

overall_design:
The impact of hormones in the thymus is observed by gene expression profiling. Differences in the responses of the thymic epithelial cells to androgens is observed using the GLYCOv2 chips, comparing samples treated vs untreated with testosterone.
At present we have analyzed by the glyco chips the differential expression of genes among sexes in thymocytes taken from female vs male mice. To have a full picture of the differences in gene expression in the thymus, thymic epithelial cells have to be analyzed. At present we have pinpointed the primary culture of these cells and their in vitro stimulation with androgens. Thus we analyzed the differential expression among testosterone treated and untreated cells.


summary:
We are currently studying how these information-carrying oligosaccharides are involved in cellular stress responses, particularly in human genetic diseases called Congenital Disorders Of Glycosylation in which oligosaccharide assembly is defective.
We are interested in endoplasmic stress responses/unfolded protein responses. ER glycans and ER lectins are intimately involved in the folding of ER proteins. Therefore, ER lectins and ER glycosyltransferases may be controlled by these stress responses, to produce and/or recognize key glycans in the stress response. Our model system is the human dermal fibroblast. We have successfully calibrated the ER stress responses in these cells by determining the magnitudes of various stress effects (such as chaperone transcription) with different forms of ER stress. We are also completing a study in which activation the signaling molecules Ire1 and ATF6 are also calibrated. We prepared multiple identical aliquots of RNA from cells stressed under several of these calibrated conditions.

overall_design: Endoplasmic reticulum (ER) stress and the unfolded protein response (UPR): Study of the role of ER stress in the expression of genes for ER transferases and lectins that participate in ER folding and quality control using human skin fibroblasts. The UPR response in these cells has been calibrated using various readouts in response to different stresses: 1) 40 nM L-azetidine-2-carboxylate (AZC) 1 hour, 2) 0.2 mg/ml castanospermine, 24 hours, 3) 2 mM Dithiothreitol (DTT), 20 minutes, 4) 100nm Thapsigargin (TG), 30 minutes, 5) 5 ug/ml tunicamycin, 5 hours, 6) untreated control cells

first: Mark

last: Lehrman


title: Gene expression in human post-mortem brain samples from schizophrenic subjects and matched controls

summary: This laboratory focuses on the molecular mechanisms of neuropsychiatric and neurodegenerative disorders

overall_design:
Gene expression patterns from the pefrontal cortical region (Brodmann Area 46) of subjects with schizophrenia and age- and sex-match control subjects was analyzed. The prefrontal cortex was chosen since it is a primary brain region implicated in the pathophysiological of schizophrenia. Furthermore, this region was used in our previous proteomics studies, allowing for the direct comparison of changes in protein levels to gene expression results.
16 schizophrenic subjects were studied, consisting of 8 subjects with duration of illness (DOI) < 5 years and 8 subjects with DOI > 22 years. 16 age- and sex-matched controls were also studied. Gene expression profiles were analyzed from individual subjects; a total of 32 samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.

first: Elizabeth

last: Thomas


title: Expression of enzymes involved in gag synthesis and degradation in cartilage aging and arthritis

summary: Glycoarrays are used to identify differences in the expression of enzymes involved in gag synthesis and degradation in cartilage aging and arthritis. This experiment includes 3 samples from donors with and without growth factor stimulation. Samples are from human biopsy/necropsy origin.

overall_design: Human knee chondrocytes were grown in monolayer culture from 3 donors unstimulated or stimulated with TGFß1 (10ng/ml) for 6 hours.

first: Matrin


title: Adult versus P7 mouse brain gene expression

summary: This laboratory studies the role of carbohydrates in the development of the central nervous system.

overall_design:
Comparison of glycosyltransferase gene expression in developing rodent cerebellum with the aim of understanding the regulation of tissue-specific glycans
RNA from adult and postnatal day 7 BALB/c mouse cerebellum was extracted and analyzed for differences in glycosyltransferase expression. Three replicate samples were processed for each age group and hybridized to the GLYCOv2 array.

first: Francis

last: Smith


title: Gene expression changes in gastric epithelial cells induced by Helicobacter pylori infection

summary:
This group is focusing on the molecular mechanisms of the biosynthesis of glycoconjugates and carbohydrate ligands important in the process of gastric carcinogenesis and on gastric carcinoma progression and metastasis.
The adhesion of H. pylori to epithelial cells induces a variety of modifications, including changes in cell morphology,cytokine production and release, alterations in glycosylation and in the biosynthesis of mucins. This study aims to identify the gene expression changes in the gastric epithelial cells (AGS) induced by Helicobacter pylori infection. This experiment was performed as previously described in the literature by submitting a gastric cell line to co-culture with reference strains of H. pylori.

overall_design: The following RNA samples (in triplicate) were analyzed by hybridization to the GLYCOv2 array: 1)Gastric cell line co-culture with H. pylori strain A(High Patogenicity) 2)Gastric cell line co-culture with H. pylori strain B(Low Patogenicity) 3)Gastric cell line without H. pylori co-culture (control)

first: Celso

last: Reis


title: Mouse Wild Type Tissue Survey

summary: Survey of gene expression in 9 types of C57/Bl mouse wild type tissue.

overall_design:
RNA was extracted from homogenized whole organs/tissues and include brain, spleen, liver, thymus, kidney, lung, testes, bone marrow, and lymph node.
8 week old male littermate C57/Bl mice

first: James

last: Paulson


title: Chronic exposure to ambient particulate matter alters cardiac gene expression patterns and markers of oxidative stress in rats

city: Los Angeles

first: Boris

middle: Z

last: Simkhovich

address: 1225 Wilshire Boulevard

department: Heart Institute

institute: Good Samaritan Hospital

summary: Exposure to ambient particulate matter (PM) significantly increases cardiovascular morbidity and mortality in the general population. We hypothesized that some components of PM can affect the gene expression patterns in the hearts of rats exposed for 3 months to filtered air (FA), coarse (CP; 2.5 < dp < 10 μm), fine (FP; dp ≤ 2.5 μm) or ultrafine (UFP; dp ≤ 0.18 μm) components of PM. The median diameters of CP, FP, and UFP were 3 μm, 0.7 μm and 0.07 μm, respectively. Exposures (n = 8 per group) were performed using a particle concentrator system in Riverside, California, an area with high ambient levels of photochemically derived gaseous and particulate pollutants. At the end of the exposure, hearts were subjected to gene expression profiling by using Illumina RatRef-12 bead chips and levels of malonaldehyde (MDA), a biomarker of oxidative stress, were measured. Applying fold ratio >1.5 (for both up- and downregulated genes), we found three genes in the CP and nine genes in the UFP groups with significantly changed expression, compared with FA. No significant changes in gene expression patterns were observed in the FP group. In the UFP group, thioredoxin-interacting protein (Txnip), a negative regulator of an antioxidant enzyme thioredoxin, and cytochrome P450 (Cyp2e1), an enzyme involved in the metabolism of foreign substances, demonstrated significant up-regulation (fold ratios 1.79 and 1.57, respectively, with false discovery rate, FDR < 0.05). In the CP group, there was also a trend towards increased Txnip expression (fold ratio 1.43, FDR > 0.05) and significant increase in the Cyp2e1 expression (fold ratio 1.79, FDR < 0.05). Changes in the Txnip and Cyp2e1 expression showed statistically significant positive correlation to each other (p < 0.0009) and were confirmed by real-time PCR. In addition, Txnip and Cyp2e1 expression demonstrated statistically significant moderate correlation with the levels of MDA in the heart. Up-regulation of both Cyp2e1 and Txnip are observed in hearts of patients with certain cardiac diseases. Therefore, chronic exposure to CP and UFP directly affects expression of disease-relevant genes in the myocardium.

overall_design: Analysis was performed on 32 microarrays (eight microarrays in each group). After five chips with poor hybridization signals were removed, the final analysis included 27 microarrays (seven miocroarrays in the FA group, six microarrays in the CP group, six microarrays in the FP group and eight microarrays in the UFP group). The Bioconductor Lumi package was used to preprocess gene chip data with default settings (Du et al. 2007; Lin et al. 2008). Probes with all samples “Absent” (lower or around background levels) were removed from further analysis. After filtering the signals, 11,657 probes on the microarray (from a total of 22,226 probes) were kept for further analysis. To identify differentially expressed genes, we applied routines implemented in the Limma package (Linear model for microarray data) to fit linear models to normalized expression values. The variance used in the t-score calculation was corrected by an empirical Bayesian method (Smyth 2004). Genes with significantly changed expression (fold ratio >1.5 for both up- and downregulated genes) were selected. The gene list was further filtered by FDR (false discovery rate) of <0.05 and <0.25, which indicate that no more than 5% and 25% of all listed genes are false positives (an assumption that is not offered by a traditional p value-based analysis).

first: Michael

middle: T

last: Kleinman

first: Ruty

last: Mehrian-Shai

first: Ya-Hsuan

last: Hsu

first: Dianne

last: Meacher

first: Glenn

last: Gookin

middle: M

last: Kinnon

first: Karina

last: Salazar

first: Paul

last: Willet

first: Gang

last: Feng

first: Simon

last: Lin

first: Robert

last: Kloner


title: MicroRNA expression of C. eleagans in space environment

status: Public on Feb 16 2011

city: Sendai

first: Atsushi

last: Higashitani

address: Katahira

department: Graduate School of Life Sciences

institute: Tohoku University

summary: The expression of 228 microRNAs, of the 232 analysed, were also unaffected during 4 and 8 d spaceflight (P>0.05).

overall_design:
Entire microRNA expression were analyzed using the Filgen® Array miRNA Caenorhabditis elegans 232 probes (Filgen). In the microRNA expression analysis, we compared the expression data between two groups: micro-gravity samples (4 d and 8 d) and controls (4 d and 8 d ground control and 1 G centrifuge onboard ISS).

CITATION:   The Effectiveness of RNAi in/Caenorhabditis elegans/Is Maintained during Spaceflight <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0020459> Timothy Etheridge, Kanako Nemoto, Toko Hashizume, Chihiro Mori, Tomoko Sugimoto, Hiromi Suzuki, Keiji Fukui, Takashi Yamazaki, Akira Higashibata, Nathaniel J. Szewczyk, Atsushi HigashitaniResearch Article, published 01 Jun 2011 doi:10.1371/journal.pone.0020459

first: Kanako

last: Nemoto


title: Gain of the oncostatin M receptor in cervical squamous cell carcinoma is associated with adverse clinical outcome [camb1Mb data]

city: Cambridge

first: Ian

last: Roberts

address: Hills Road

department: Cancer Cell Unit

country: United Kingdom

institute: Hutchison MRC Research Centre

type: Genome variation profiling by genome tiling array

summary: For many oncogenes, increased expression resulting from copy number gain confers a selective advantage to cells that consequently make up the tumour bulk. To identify oncogenes of potential biological significance in cervical squamous cell carcinoma (SCC), 36 primary samples and ten cell lines were screened by array comparative genomic hybridization (CGH). The most commonly occurring regions of copy number gain that also showed amplification were 5p15.2–14.3 (59%), 5p13.3 (65%), and 5p13.2–13.1 (63%). Gene copy numbers were significantly associated with expression levels for three candidate oncogenes at these loci: OSMR (oncostatin M receptor) (p = 0.03), PDZK3 (PDZ domain containing protein 3) (p = 0.04), and TRIO (triple functional domain) (p = 0.03). Further examination by fluorescence in situ hybridization on a tissue microarray of 110 primary cervical SCC samples revealed copy number gain frequencies of 60.9%, 57.3%, and 54.5% for OSMR, PDZK3, and TRIO, respectively, with OSMR adversely influencing overall patient survival independently of tumour stage (p = 0.046). By array CGH, copy number gain of OSMR was not seen in any of 40 microdissected precursor cervical squamous intraepithelial lesions (SILs). Moreover, global mRNA expression analysis, using Affymetrix U133A 2.0 Arrays, showed no overexpression of OSMR in SILs, suggesting that OSMR gain and overexpression are relatively late steps in cervical carcinogenesis. In the cervical SCC cell lines CaSki and SW756, exogenous OSM activated downstream-signalling elements of OSMR including STAT3, p44/42 MAPK, and S6 ribosomal protein, and induced transcription of the angiogenic factor VEGF, effects that were reduced by OSMR depletion using RNA interference. We conclude that copy number gain of OSMR is frequently found in cervical SCC and is associated with adverse clinical outcome. As well as being a potential prognostic marker, OSMR is a candidate cell surface therapeutic target

overall_design: aCGH of high grade late stage primary cervical SCCs obtained from the archives of the Kidwai Memorial Institute of Oncology,

first: Grace

last: Ng

first: David

last: Winder

first: Balaji

last: Muralidhar

first: Emma

middle: L

last: Gooding

first: Mark

last: Pett

first: Geeta

last: Mukherjee

first: J

last: Huang

first: Nicholas

last: Coleman


title: Canary Ovarian Cell Line Gene Expression

status: Public on Feb 12 2011

city: Stanford

first: Patrick

middle: O

last: Brown

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine

summary: All cell lines were cultured according to the specifications outlined by ATCC. Cell lines were grown to 80% confluence, then serum-deprived in 0.5% FBS for 24 hours before harvesting. Cells were washed twice with Hank's Balanced Salt Solution (Invitrogen, Carlsbad, California) and drained. 1 mL of SDS extraction buffer (0.1M NaCl, 20 mM Trizma base, 25 mM EDTA, 0.5% w/v SDS) was added directly to the plate to lyse the cells. Cellular lysate was scraped off the plates, pipetted into a cryovial, and stored at 80C until DNA extraction. Lysates were treated with 200 ug/ml ProteinaseK at 50C overnight. DNA was precipitated with one volume of Isopropanol and dissolved in TE4 buffer.  Cell lines were lysed in Phenol followed by a Phenol/Chloroform extraction. The aqueous layer was added to 70% ethanol and further purified by loading the RNA/Ethanol mix into an RNeasy Mini kit (Qiagen) column. Purification was continued and finalized as described in the RNeasy kit (Qiagen) Manual.  We measured transcript levels in the 27 primary ovarian tumors and 15 cell lines using the HEEBO [16] oligonucleotide microarrays, containing 44,544 70-mer probes and printed at the Stanford Functional Genomics Facility. Detailed information on the HEEBO arrays is available at the Stanford Functional Genomics Facility website. Experimental methods.  Microarray experiments were performed as described at the Brown lab website. Briefly, 500 ug of total RNA from each of the ovarian tumors were amplified using Amino Allyl Message Amp II aRNA Kit (Ambion, Austin, TX, USA). The aRNAs were labeled with Cy5 and co-hybridized with Cy3 labeled Stratagene reference aRNA. For some samples, the mRNA was amplified and hybridized in duplicate or triplicate. The samples were then hybridized to HEEBO microarrays. The arrays were scanned in a low-ozone environment using a GenePix 4000A microarray scanner and images were analyzed with Genepix 5.0 (Axon instruments, Union City, CA).

overall_design: Using regression correlation

first: Mari

last: Olsen


title: Transcriptional plasticity of a soil arthropod across different ecological conditions

status: Public on Feb 15 2011

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

summary: It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated.

overall_design: Test animals were exposed to 26 natural soils + 2 control soils. 4 biological replicates per soil containing 25 grams of soil and 30 23-day-old animals per replicate, RNA was isolated after two days of exposure. for the micro-array hybridization design we made use of an interwoven loop design. from the four replicates per soil two were labeled with Cy3 and 2 with Cy5. It was made sure that now two replicates of the same soil were ever hybridized against the same soil.

first: Adriana

last: Birlutiu

first: Zoltan

last: Bochdanovits

first: Martijn

middle: J

last: Timmermans

first: Tjeerd

last: Dijkstra

first: Nico

last: van Straalen

first: Bauke

last: Ylstra

first: Dick

last: Roelofs


title: Gain of the oncostatin M receptor in cervical squamous cell carcinoma is associated with adverse clinical outcome [penn1Mb data]

first: Ian

last: Roberts

overall_design: 36 primary cervical SCC samples, and 10 cervical SCC cell lines were subject to 1 Mb aCGH using a dye swapped approach. Two samples were subject to repeat.  (J Pathol. 2007 Jul;212(3):325-34.)

first: Grace

last: Ng

first: David

last: Winder


title: Global transcriptional response to copper of Enterococcus faecalis  wild-type and copY mutant

status: Public on Feb 14 2011

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

summary: We examined the whole-genome transcriptional response of E. faecalis wild-type (WT) and copy mutant cells exposed to non toxic Cu excess. The analysis was focused in those genes which changed significantly their expression levels in the Cu-treated cells when compared to their untreated counterparts. The results indicated that after 3 h at 0.5 mM CuSO4, WT cells exhibited a significant increment of Cu content and the induction of three genes of cop operon along with other 142 genes. The comparison with the copY mutant exposed to Cu showed an extensive overlapping of transcriptional changes suggesting that other transcription factors may be mediating the response to Cu. Associated manuscript The global response of Enterococcus faecalis to copper exposure

overall_design: RNA was extracted from four different culture conditions:  1) untreated WT cells; 2) Cu-treated WT cells; 3) untreated copy mutant cells; and 4) Cu-treated copy mutant cells. Each array contained 72,000 oligonucleotides 60-mer, with an average of 11 oligos designed for the 3,114 open reading frames of E. faecalis V583, that represent twice the genome of the bacterium (two technical replicates per arrays). For wild type and copY mutant four independent hybridizations (two biological replicates per treatment paired with their respective controls) were performed. Gene expression data from WT cells was compared to Cu-treated WT cells; and data from copY mutant cells were compared to Cu-treated copY mutant cells.

first: Angelica

last: Reyes-Jara

first: Guadalupe

last: Lopez

last: González


title: Identification of differentially expressed genes associated with semigamy in Pima cotton

city: Las Cruces

first: Laura

last: Rodriguez-Uribe

state: NM

address: 945 College Dr. Skeen Hall RM 127

department: Plant and environmental Sciences

institute: New Mexico State University

summary: The comparative analysis between 57-4 and Pima S-1 identified 284 genes in anthers and 1,864 genes in ovules as being differentially expressed in the semigametic genotype. Based on gene functions, 127 differentially expressed genes were common to both semigametic anthers and ovules, with 115 being consistently differentially expressed in both tissues.  Nine of those genes were selected for qRT-PCR analysis, seven of which were confirmed.  Furthermore, several well characterized metabolic pathways including glycolysis/gluconeogenesis, carbon fixation in photosynthetic organisms, sesquiterpenoid biosynthesis, and the biosynthesis of and response to plant hormones were shown to be affected by differentially expressed genes in the semigametic tissues.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Anther and ovule tissues from 10 flowers of 57-4 and Pima S-1 was collected at zero days postanthesis (0 DPA) and placed in liquid nitrogen and stored at -80 °C. Total RNA was isolated using a hot borate method and cRNA was hybridized to the Affymetrix Cotton Genome GeneChips.

first: Jessica

last: Curtiss

first: J

last: Stewart

first: Jinfa

last: Zhang


title: Ovarian Tumor Tissue Expression Study

first: Patrick

last: Brown

summary: Ovarian tumor tissues were obtained from patients with informed consent, which was approved by the Institutional Review Board of the Swedish Hospital in Seattle.  Tissue acquisition, processing and storage were conducted by the Pacific Ovarian Cancer Research Consortium (POCRC) at the Fred Hutchinson Cancer Research Center. The quality of tumor tissues, the percentage of cancer cells and the histological analysis of the tumors were determined via a centralized pathology review at the POCRC repository. All samples were distributed in a de-identified manner and cannot be traced back to patients.    The tumor tissues were disrupted in a Biospec Tissue-Tearor Model 985370-395 in the presence of TRIzol (Invitrogen) with a ratio of 10ml TRIzol per 50mg of tissue. Following an extraction step of 0.2 ml of Chloroform per 1ml of TRIzol, the upper aqueous phase was removed for RNA isolation.  The remaining inter-phase and the phenol phase was briefly stored in 4??C for DNA isolation. The upper aqueous phase was processed for total RNA according to Invitrogen protocol and further purified using RNeasy Mini kit (Qiagen). Genomic DNA was isolated by back-extraction from the TRIzol inter-phase and the phenol phase as described on Ambion website (page 4). Detailed amplification and labeling protocols are available at the Brown lab website

first: Mari

last: Olsen


title: Transcriptional profile of human liver tissues: hepatocellular carcinoma vs. matched noncancerousliver tissue

city: Guangzhou

first: Qingming

last: Zhou

state: Guangdong

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University

summary: Transcriptional profiling of  hepatocellular carcinoma vs. matched noncancerous liver tissue

overall_design: 81 pairs of  hepatocellular carcinoma and matched noncancerousliver tissues

first: Binkui

last: Li

first: Guoliang

last: Huang

first: Rongrong

last: Wei

first: Meiyin

first: Xiaoqian

last: Chen

first: Long

first: Yunfei

last: Yuan

first: Ming

last: Shi

first: Huizhong

first: Bijun

first: Guohong

last: Hu

first: Xianrong

last: Luo

first: Huiyun

last: Wang


title: NK cells and immune memory

status: Public on Feb 11 2011

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

institute: University of California, San Francisco

summary: Microarray profiling of adoptively transferred GFP-marked NK cells during MCMV infection in C57BL/6 mice

overall_design: Multiple independent replicates were collected per time point.  NK cells were isolated from spleens of mice by flow cytometry.  RNA isolated, amplified, and hybridized as two-color experiment against a common pooled reference.

first: Charles

middle: C

first: Joseph

last: Sun

first: Sandra

last: Lopez-Verges

last: DeRisi

first: Lewis

last: Lanier


title: IGH analysis in pro-B cells with H3K4me3, H3K4me2, H3K9ac, H3K27me3, Pax5 and CTCF [ChIP-chip]

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

summary: VH-DJH recombination of the immunoglobulin heavy-chain (Igh) locus is temporally and spatially controlled during early B-cell development, and yet no regulatory elements other than the VH gene promoters have been identified throughout the entire 2.5-Mb VH gene cluster. Here we discovered novel regulatory sequences that are interspersed in the distal VH gene region. These conserved repeat elements were characterized by the presence of Pax5-dependent active chromatin, the binding of Pax5, E2A, CTCF and Rad21 as well as by Pax5-dependent antisense transcription in pro-B cells. The Pax5-activated intergenic repeat (PAIR) elements were no longer bound by Pax5 in pre-B and B cells consistent with the loss of antisense transcription, whereas E2A and CTCF interacted with PAIR elements  throughout early B-cell development. The pro-B-cell-specific and Pax5-dependent activity of the PAIR elements suggests that they are involved in the regulation of distal VH-DJH recombination at the Igh locus.

overall_design: Analysis of chromatin and TF binding in rag2-/- and pax5-/- rag2-/- pro-B cells. Chip-Chip with one experiment for each antibody, 12 samples.

first: Shane

last: McManus

first: Anja

last: Ebert

first: Maria

last: Novatchkova

first: Markus

last: Jaritz


city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary:
Genome-wide gene expression atlas of maize inbred line B73.  Maize inbred B73 was used for constructing the gene atlas. Plants were grown in Plano silt loam soil at the West Madison Agricultural Research Station, Verona, WI during Summer 2008. During field preparation, 200 kg/acre of Urea (46-0-0) was applied. One day after planting, herbicides including Callisto (142 g/acre), Dual II (710 ml/acre), and Simazine (227 g/acre) were applied. For collection of seed tissues, shoots were covered before silk emergence avoiding any injury to the plants. Plants were self-pollinated on the same day to establish a common time initiation point for the harvest timeline. Greenhouse-grown plants were propagated by growing five plants per pot (30 cm top diameter, 28 cm height, 14.5 L volume) containing Metro-Mix 300 (Sun Gro Horticulture, Bellevue, WA, USA) with no additional fertilization. The growing conditions were 27 deg. C day and 24 deg. C night temperature with a 16h light (5:00am to 9:00pm) and 8h dark regime. Germinating seed tissue was generated by soaking seeds in distilled water in a Petri dish for 12h and then placing seeds between layers of moist paper towels for another 12h to allow germination. The field samples were collected between 8:00am and 10:00am, approximately 3 hours after sunrise. The greenhouse samples were collected between 8:00am and 9:00am, three hours after turning on the lights. Three biological replicates were collected for each tissue type. For all the tissues except germinating seeds, a biological replicate was constituted by collecting and pooling samples from three competitive randomly chosen plants. For germinating seed, ten randomly chosen seeds were pooled to form a biological replicate. The harvested tissues were immediately frozen in liquid nitrogen and stored at -80 deg. C. Total RNA was extracted using TRIZOL reagent (Invitrogen, http://www.invitrogen.com) following the manufacturer's protocol, and purified using RNeasy MinElute Cleanup Kit (Qiagen, http://www.qiagen.com) following the manufacturer's instructions.

PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Rajandeep S Sekhon. The equivalent experiment is ZM29 at PLEXdb.

overall_design: organism part name: 24H_Germinating Seed(3-replications);  organism part name: 6DAS_GH_Coleoptile(3-replications);  organism part name: 6DAS_GH_Primary Root(3-replications);  organism part name: V1_GH_Primary Root(3-replications);  organism part name: VE_Whole Seedling(3-replications);  organism part name: VE_Primary Root(3-replications);  organism part name: V1_Pooled Leaves(3-replications);  organism part name: V1_Stem and SAM(3-replications);  organism part name: V4_Stem and SAM(3-replications);  organism part name: V3_Stem and SAM(3-replications);  organism part name: V3_First Leaf and Sheath(3-replications);  organism part name: V3_Topmost Leaf(3-replications);  organism part name: V5_Shoot Tip(3-replications);  organism part name: V5_First Internode(3-replications);  organism part name: V5_Tip of stage-2 Leaf(3-replications);  organism part name: V5_Base of stage-2 Leaf(3-replications);  organism part name: V7_First Internode(3-replications);  organism part name: V7_Tip of stage-2 Leaf(3-replications);  organism part name: V7_Base of stage-2 Leaf(3-replications);  organism part name: V9_Fourth Internode(3-replications);  organism part name: V9_Eighth Leaf(3-replications);  organism part name: V9_Eleventh Leaf(3-replications);  organism part name: V9_Thirteenth Leaf(3-replications);  organism part name: V9_Immature Leaves(3-replications);  organism part name: V13_Immature Tassel(3-replications);  organism part name: V18_Meiotic Tassel(3-replications);  organism part name: V18_Immature Cob(3-replications);  organism part name: VT_Thirteenth Leaf(3-replications);  organism part name: R1_Pre-pollination Cob(3-replications);  organism part name: R1_Silks(3-replications);  organism part name: R1_Anthers(3-replications);  organism part name: R1_Innermost Husk(3-replications);  organism part name: R2_Thirteenth Leaf(3-replications);  organism part name: R2_Outer Husk(3-replications);  organism part name: R2_Innermost Husk(3-replications);  organism part name: 2DAP_Whole Seed(3-replications);  organism part name: 4DAP_Whole Seed(3-replications);  organism part name: 6DAP_Whole Seed(3-replications);  organism part name: 8DAP_Whole Seed(3-replications);  organism part name: 10DAP_Whole Seed(3-replications);  organism part name: 12DAP_Whole Seed(3-replications);  organism part name: 12DAP_Endosperm(3-replications);  organism part name: 14DAP_Whole Seed(3-replications);  organism part name: 14DAP_Endosperm(3-replications);  organism part name: 16DAP_Whole Seed(3-replications);  organism part name: 16DAP_Endosperm(3-replications);  organism part name: 16DAP_Embryo(3-replications);  organism part name: 18DAP_Whole Seed(3-replications);  organism part name: 18DAP_Endosperm(3-replications);  organism part name: 18DAP_Embryo(3-replications);  organism part name: 18DAP_Pericarp(3-replications);  organism part name: 20DAP_Whole Seed(3-replications);  organism part name: 20DAP_Endosperm(3-replications);  organism part name: 20DAP_Embryo(3-replications);  organism part name: 22DAP_Whole Seed(3-replications);  organism part name: 22DAP_Endosperm(3-replications);  organism part name: 22DAP_Embryo(3-replications);  organism part name: 24DAP_Whole Seed(3-replications);  organism part name: 24DAP_Endosperm(3-replications);  organism part name: 24DAP_Embryo(3-replications)

first: Rajandeep

middle: S

last: Sekhon


title: Molecular Characterization of In Vivo Adjuvant Activity in Ferrets Vaccinated against Influenza Virus

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

summary: The 2009 H1N1 influenza pandemic has prompted a significant need for the development of efficient, single-dose, adjuvanted vaccines. Here we investigated the adjuvant potential of CpG oligodeoxynucleotide (ODN) when used with a human seasonal influenza virus vaccine in ferrets. We found that the CpG ODNadjuvanted vaccine effectively increased antibody production and activated type I interferon (IFN) responses compared to vaccine alone. Based on these findings, pegylated IFN- 2b (PEG-IFN) was also evaluated as an adjuvant in comparison to CpG ODN and complete Freund’s adjuvant (CFA). Our results showed that all three vaccines with adjuvant added prevented seasonal human A/Brisbane/59/2007 (H1N1) virus replication more effectively than did vaccine alone. Gene expression profiles indicated that, as well as upregulating IFN-stimulated genes (ISGs), CpG ODN enhanced B-cell activation and increased Toll-like receptor 4 (TLR4) and IFN regulatory factor 4 (IRF4) expression, whereas PEG-IFN augmented adaptive immunity by inducing major histocompatibility complex (MHC) transcription and Ras signaling. In contrast, the use of CFA as an adjuvant induced limited ISG expression but increased the transcription of MHC, cell adhesion molecules, and B-cell activation markers. Taken together, our results better characterize the specific molecular pathways leading to adjuvant activity in different adjuvant-mediated influenza virus vaccinations.

overall_design: In this experiment, 3 ferrets in each group immunizied with different adjuvanted human seasonal vaccines of CFA plus vaccine, CpG plus vaccine, pegylated IFN-alpha plus vaccine and vaccine alone (PBS plus vaccine) and 4 ferrets from control group (PBS only) were anesthetized at day 1 post vaccination.  The whole blodd was collected for RNA extraction and purification on the scheduled date. The subsequent gene expression analysis was performed with Affymetrix GeneChip Canine Genome 2.0 Array.

first: David

last: Kelvin


title: MicroRNAs characterize genetic diversity and drug resistance in pediatric acute lymphoblastic leukemia

city: Rotterdam

first: Monique

last: Den Boer

address: POBox 2060

department: Pediatric Oncology

institute: Erasmus MC-Sophia Children's Hospital

summary:
MicroRNAs (miRNAs) regulate activity of protein-coding genes including those involved in hematopoietic cancers. The goal of the current study was to explore which miRNAs are unique for seven different subtypes of pediatric acute lymphoblastic leukemia (ALL). Therefore, the expression levels of 397 miRNAs (including novel miRNAs) were measured by quantitative RT-PCR in 81 pediatric leukemia cases and 17 normal hematopoietic control cases.
Except for BCR-ABL-positive and B-other ALL, all major subtypes i.e. T-ALL, MLL-rearranged, TEL-AML1-positive, E2A-PBX1-positive and hyperdiploid ALL have unique miRNA-signatures that differ from each other and from those in healthy hematopoietic cells. Strikingly, the miRNA signature between TEL-AML1-positive and hyperdiploid cases partly overlapped, which suggests a common underlying biology. Moreover, aberrant downregulation of let-7b (~70-fold) in MLL-rearranged ALL was linked to upregulation of oncoprotein c-Myc (P<0.0001). Besides genetic aberrations, in vitro drug resistance predicts clinical outcome. Resistance to vincristine and daunorubicin was characterized by ~20-fold upregulation of miR-125b, miR-99a and miR-100 (P≤0.002). No discriminative miRNAs were found for prednisolone and only one miRNA was linked to L-asparaginase resistance. Finally we show that the expression levels of 14 miRNAs were --independently of subtype-- associated with clinical outcome in pediatric ALL.
We conclude that genetic subtypes and drug resistant leukemic cells display characteristic miRNA signatures in pediatric ALL. Functional studies of discriminative and prognostic important miRNAs may provide new insights into the biology of disease.
Experiment type: stem-loop real-time (RT) quantitative PCR (RT-qPCR)

overall_design:
Bone marrow and peripheral blood samples were collected from children at newly diagnosis of acute lymphoblastic leukemia (ALL). CD34+ -cells were sorted from G-CSF-stimulated blood cell samples of children with a brain tumor or Wilm’s tumor. Thymocytes were isolated from thymic lobes that were resected from children during surgery for congenital heart disease. RNA from the cell samples was extracted using TRIzol reagents (firma). Only RNA with an RNA Integrity Number (RIN) of  ≥ 7.5 as measured by the 2100 Bioanalyzer (Agilent, Amstelveen, the Netherlands) was used as input for the RT-qPCR reactions.
All miRNAs were validated with the stem-loop real-time (RT) quantitative PCR (RT-qPCR) technique by using either TaqMan MicroRNA Array MicroRNA arrays (v 1.0, Early Access) or Custom TaqMan MicroRNA Array arrays (Applied Biosystems, Foster City, USA). Values represent ∆Ct in each individual patient for whom the specific subtype, identification number and cellular drug-resistance is shown on top of each column. Drug-resistance was based on median LC50 values (concentration of a drug lethal to 50% of the leukemic cells) that have reported prognostic impact in children with newly diagnosed ALL. Median LC50 values were used to assign patients as sensitive (≤ median LC50) or resistant (> median LC50) to the drug in question. The ∆Ct value was calculated according to the following equation: Ct value of the specific miRNA minus the Ct value of the internal reference. In case of the TaqMan MicroRNA Array MicroRNA arrays the mean Ct values for snoR-13 and snoR-14 were used as reference whereas in case of the Custom TaqMan MicroRNA Array arrays snoR-1 was used.  MiRNAs validated by the TaqMan MicroRNA Array MicroRNA arrays are listed together with the part numbers of the corresponding (stem-loop) primers as available by Applied Biosystems, Foster City, USA. Primers for the remaining miRNAs were custom designed by Applied Biosystems.
Abbreviations: MLL: MLL-rearranged precursor B-ALL, B-other: precursor B-ALL negative for MLL-rearrangements, TEL-AML1, BCR-ABL, E2A-PBX and hyperdiploidy (> 50 chromosomes). CD34+: normal CD34+-sorted blood progenitor cells, nBM: normal bone marrow.

first: Diana

last: Schotte

last: den Boer


title: Large scale screening for known fusion genes in cancer cell lines

status: Public on Feb 10 2011

city: Oslo

first: Gard

middle: Olav

last: Thomassen

address: Radiumhospitalet, Rikshospitalet HF

department: Institute for Cancer Research

country: Norway

institute: Rikshospitalet

type:
Expression profiling by array
Genome variation profiling by array

summary:
We have utilized a version 2.0 of our Fusion gene microarray (version 1.0 described by PMID: 19152679 and GEO, GPL8078) to screen cancer cell lines for known fusion genes
We assembled a comprehensive database of published fusion genes, including those which have been reported only in individual studies and samples, and fusion genes resulting from deep sequencing of cancer genomes and transcriptomes. From the total set of 548 fusion genes, we designed 197,846 unique oligonucleotides, targeting both chimeric transcript junctions as well as sequences internal to each of the fusion gene partners. We investigated the presence of fusion genes in a series of 67 cell lines originating from 15 different cancer types. Data from ten leukaemia cell lines with known fusion gene status were used to evaluate and calibrate an automated scoring algorithm. In five out of ten cell lines the correct fusion gene was the top most scoring hit, and one came second, all six passing a cut-off of 50 percent of theoretical maximum-score. Two additional fusion genes, BCAS4-BCAS3 from the MCF-7 breast cancer cell line and CCDC6-RET from the TPC-1 thyroid cancer cell line were validated as true positive fusion transcripts from the remaining 57 cell lines.

overall_design: A total of 67 cell lines from various cancer types were analysed for presence of known fusion genes

first: Marthe

last: Løvf

first: Anne

last: Bakken

first: Ricardo

last: Celestino

first: Thoas

last: Fioertos

first: Guro

middle: E

last: Lind

first: Ragnhild

last: Lothe

first: Rolf

middle: I

last: Skotheim


title: Comparison of CD133 high and CD133 negative cell populations isolated from colorectal carcinoma and liver metastases

city: Heidelberg

first: Aurelie

last: Ernst

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

summary: Microarray-based gene expression analysis identified genes differentially expressed between CD133 high and CD133 negative cell populations isolated from colorectal carcinoma and liver metastases

overall_design: In this study, a set of 5 colorectal cancers was used to acquire expression profiles, leading to the identification of differentially expressed genes between CD133 high and CD133 negative cell populations by Significance Analysis of Microarray dada.

first: Aurélie

first: Felix

last: Engel


title: Mitochondrial mutations in cigarette smoke extract-chronically treated human oral OKF6 cells

city: Baltimore

first: wenyue

last: sun

address: 1550 Orleans street, Rm 574A

department: Otolaryngology Head and Neck Surgery

institute: Johns Hopkins Medical Institutions

summary:
The objective of this study was to analyze the mitochondrial mutations induced by chronic cigarette smoke extract treatment in human oral immortal OKF6 cells.
The objective of this study was to analyze the mitochondrial mutations induced by chronic cigarette smoke extract treatment in human oral immortal OKF6 cells.

overall_design: 2 samples were included, a control passaged human oral immortal OKF6 cells and cigarette smoke extract-treated OKF6 cells.  The chronic treatment for cigarette smoke extract is 7 months. Genomic DNAs were extracted from both cells and then used for Affymetix MitoChip Version 2.0 analysis.

first: Wenyue

last: Sun

first: Steven

last: Chang

first: Yumei

last: Fu

first: Yan

last: Liu

first: Joseph

last: Califano


title: Microarray Analysis of Infective and Noninfective Larvae of Strongyloides stercoralis

status: Public on Feb 09 2011

city: Bethesda

first: Roshan

last: Ramanathan

address: 4 Center Drive

department: NIAID

institute: National Institutes of Health

summary: BACKGROUND: Differences between noninfective first-stage (L1) and infective third-stage (L3i) larvae of parasitic nematode Strongyloides stercoralisat the molecular level are relatively uncharacterized. DNA microarrays were developed and utilized for this purpose. METHODS AND FINDINGS: Oligonucleotide hybridization probes for the array were designed to bind 3571 putative mRNA transcripts predicted by analysis of 11,335 expressed sequence tags (ESTs) obtained as part of the Nematode EST project. RNA obtained from S. stercoralis L3i and L1 was co-hybridized to each array after labeling the individual samples with different fluorescent tags. Bioinformatic predictions of gene function were developed using a novel cDNA Annotation System software. We identified 967 differentially expressed genes (457 L3i-biased; 510 L1-biased) having greater than two-fold expression differences and p < 0.01. Based on functional analysis, L1s have a larger number of genes putatively involved in transcription (p = 0.0158), and L3is have higher expression of stress-related genes (such as putative heat shock proteins dnj-12, daf-21, dnj-10). Genes with products that have been shown to be immunoreactive in S. sterocoralis-infected humans (SsIR and NIE) were additionally found to be L3i biased. Unique and abundant L3i contigs of interest included S. stercoralis orthologs of cytochrome oxidase ucr 2.1, daf-12, and daf-21, which may be potential chemotherapeutic targets. The S. stercoralis ortholog of fatty acid and retinol binding protein-1, successfully used in a vaccine against Ancylostoma ceylanicum, was identified among the top 25 most L3i-biased genes. The sperm-containing glycoprotein domain, utilized in a vaccine against the nematode Cooperia punctata, was exclusively found in the L3i group and may be a valuable S. stercoralis target of interest. Conclusions A new DNA microarray tool for the examination of S. stercoralis biology has been developed and provides new and valuable insights regarding differences between infective and noninfective S. stercoralis larvae. Potential therapeutic and vaccine targets were identified for further study.

overall_design: For the present study, four technical replicates using pooled samples of L1 stage larvae versus L3i stage larvae were performed, including one dye swap.


title: Mapping of H3K4 and H3K27 trimethylation in zebrafish cells (ChIP-chip)

status: Public on Feb 08 2011

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

institute: University of Oslo

summary: The genomic distribution of post-translationally modified histones in the zebrafish (Danio rerio) genome remain largely unraveled. The objective of this study was to (1) design a microarray covering all zebrafish gene promoters and 5' end of coding regions, and (ii) using these arrrays, map the genome-wide distribution of trimethylated H3K4 and H3K27 in the mbryo derived ZF4 cell line.  Specifically, we determined teh enrichment profile of H3K4me3, H3K27me3 and of both (co-enriched) modifications in ZF4 cells. We determined average enrichment profiles through metagene analysis, functional terms enriched among genes marked by either modification, and pathway analysis.

overall_design: ChIP-chip experiments were performed from duplicate cultures

first: P

first: A

middle: H

last: Reiner

first: L

last: Lindeman


title: Genome-wide gene expression profiling on pre-chemotherapy biopsies of osteosarcoma patients who developed metastases within 5yrs (n=34) and patients who did not develop metastases within 5yrs (n=19)

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

institute: Centre for Molecular Medicine Norway

summary: High-grade osteosarcoma is a malignant primary bone tumor with a peak incidence in puberty. Overall survival of patients with metastatic disease is approximately twenty percent. Mechanisms behind the development of metastases in osteosarcoma are unknown. To identify gene signatures that play a role in metastasis, we performed genome-wide gene expression profiling on pre-chemotherapy biopsies of osteosarcoma patients who developed metastases within 5yrs and patients who did not develop metastases within 5yrs.

overall_design: Pre-chemotherapy biopsies of osteosarcoma patients who developed metastases within 5yrs (n=34) were compared with pre-chemotherapy biopsies of osteosarcoma patients who did not develop metastases within 5yrs (n=19).


title: Mapping of H3K4 and H3K27 trimethylation in zebrafish cells (Gene expression)

summary: The genomic distribution of post-translationally modified histones in the zebrafish (Danio rerio) genome remain largely unraveled. The objective of this study was to (1) design a microarray covering all zebrafish gene promoters and 5' end of coding regions, and (ii) using these arrrays, map the genome-wide distribution of trimethylated H3K4 and H3K27 in the embryo derived ZF4 cell line.  Specifically, we determined the enrichment profile of H3K4me3, H3K27me3 and of both (co-enriched) modifications in ZF4 cells. We determined average enrichment profiles through metagene analysis, functional terms enriched among genes marked by either modification, pathway analysis, and in relation to gene expression.

overall_design: Gene expression experiments were performed on three biological replicates.


title: The effect of antibiotic treatment on the intestinal metabolome

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

department: Michael Smith Laboratories

institute: The University of British Columbia

summary:
The importance of the mammalian intestinal microbiota to human health has been intensely studied over the past few years. It is now clear that the interactions between human hosts and their associated microbial communities need to be characterized in molecular detail if we are to truly understand human physiology. Additionally, the study of such host-microbe interactions is likely to provide us with new strategies to manipulate such complex systems to maintain or restore homeostasis in order to prevent or cure pathological states.
We describe the use of high-throughput metabolomics to shed light on the interactions between the intestinal microbiota and the host. We show that treatment with the antibiotic streptomycin disrupts intestinal homeostasis and has a profound impact on the intestinal metabolome, affecting the levels of over 87% of all metabolites detected. Many metabolic pathways that are critical for host physiology were affected, including bile acid, eicosanoid and steroid hormone synthesis. Interestingly, many of these pathways are also affected by intestinal pathogens. Dissecting the effect of both beneficial and pathogenic bacteria on some of these pathways will be instrumental in understanding the interplay between the host, the resident microbiota and incoming pathogens and may aid in the design of new therapeutic strategies that target these interactions.

overall_design: Age-matched female C57BL/6 mice were used. Fresh feces were collected and stored at -80 oC. Mice were then treated with 20 mg of streptomycin through oral gavage and fresh feces were collected 24 hours after treatment and stored at -80 oC until used. To extract metabolites from feces, acetonitrile was added to samples (approximately 10-25 μL of acetonitrile per 1 mg of tissue), which were then homogenized. The samples were then cleared by centrifugation and the supernatant was collected and dried at room temperature using a centrifuge equipped with a vacuum pump. All extracts were kept at -80 oC until used. For metabolic profiling, the dried extracts from mouse feces were suspended in a 2:3 mixture of water and acetonitrile (10 μL per 1 mg of tissue), vortexed and cleared by centrifugation. Supernatants were collected and used as described below. Extracts were diluted 1:5 with 60% acetonitrile containing either 0.2% formic acid (for positive ion mode) or 0.5% ammonium hydroxide (for negative ion mode) and spiked with predefined amounts of the "ES tuning mix" solution as the internal standard for mass calibration. The solutions were then infused, using a syringe pump (KDS Scientific, Holliston, USA) at a flow rate of 2.5 µL per minute, into a 12-T Apex-Qe hybrid quadrupole-FT-ICR mass spectrometer (Bruker Daltonics, Billerica, USA) equipped with an Apollo II electrospray ionization source, a quadrupole mass filter and a hexapole collision cell. Data were recorded in positive and negative ion modes with broadband detection and an FT acquisition size of 1024 kilobytes per second, within a range of m/z 150 to 1100. Under these settings, a mass resolution of ca. 100,000 (full width at half maximum, FWHM) at m/z 400 and a mass accuracy within 2 ppm or less for all detected components, following internal mass calibration, were observed. Other experimental parameters were: capillary electrospray voltage of 3600-3750 V, spray shield voltage of 3300-3450 V, source ion accumulation time of 0.1 s and collision cell ion accumulation time of 0.2 s. To increase detection sensitivity, survey scan mass spectra in positive and negative ion modes were acquired from the accumulation of 200 scans per spectrum, and duplicate acquisitions per sample were carried out to ensure data reproducibility. Raw mass spectrometry data were processed as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140). To identify differences in metabolite composition between untreated and treated samples, we first filtered our list of masses for metabolites that were present on one set of samples (untreated or treated) but not the other. Additionally, we averaged the mass intensities of metabolites in each group and calculated the ratios between averaged intensities of metabolites from untreated and treated samples. To assign possible metabolite identities to the masses present in only one of the sample groups or showing at least a 2-fold change in intensities between the sample groups, the monoisotopic neutral masses of interest were queried against MassTrix (http://masstrix.org), a free-access software designed to incorporate masses into metabolic pathways. Masses were searched against the Mus musculus database within a mass error of 3 ppm. Data were analyzed by unpaired t tests with 95% confidence intervals.

first: Jun

last: Han

first: Rosana

last: Ferreira

first: Petra

last: Lolić

first: Christoph

last: Borchers

first: B

last: Finlay


title: Determination of the FarR regulon

city: Wuerzburg

first: Stephanie

last: Schielke

address: Josef-Schneider-Str. 2 / E1

department: Institute for Hygiene and Microbiology

institute: University of Wuerzburg

summary: Whole genome DNA microarray of Neisseria meningitidis serogroup B strain MC58 and the isogenic mutant strain deficient of the transcriptional regulator FarR, MC58 ∆farR.

overall_design: Wild type MC58 and the farR deficient mutant strain MC58 ∆farR were grown to mid-exponential growth phase in three independent experiments. The bacterial RNA was extracted and transcribed to cDNA, which was, each with dye-swap pairs, hybridized to the microarray slides.

first: Carolin

last: Spatz

first: Roland

last: Schwarz

first: Biju

last: Joseph

last: Schoen

first: Sabine

last: Schulz

first: Kerstin

last: Hubert

first: Matthias

last: Frosch

first: Alexandra

last: Schubert-Unkmeir

first: Oliver

last: Kurzai


title: A metabolomics analysis of Salmonella infection

summary:
The interplay between pathogens and hosts has been studied for decades using targeted approaches such as the analysis of mutants and host immunological responses. Although much has been learned from such studies, they focus on individual pathways and fail to reveal the global effects of infection on the host. To alleviate this issue, high-throughput methods such as transcriptomics and proteomics have been used to study host-pathogen interactions. Recently, metabolomics was established as a new method to study changes in the biochemical composition of host tissues.

We report a metabolomics study of Salmonella enterica serovar Typhimurium infection. We used Fourier Transform Ion Cyclotron Resonance Mass Spectrometry with Direct Infusion to reveal that dozens of host metabolic pathways are affected by Salmonella in a murine infection model. In particular, multiple host hormone pathways are disrupted. Our results identify unappreciated effects of infection on host metabolism and shed light on mechanisms used by Salmonella to cause disease, and by the host to counter infection.

overall_design: Female C57BL/6 mice were infected with Salmonella enterica serovar Typhimurium SL1344 cells by oral gavage. Feces and livers were collected and metabolites extracted using acetonitrile. For experiments with feces, samples were collected from 4 mice before and after infection. For liver experiments, 11 uninfected and 11 infected mice were used. Samples were combined into 3 groups of 3-4 mice each, resulting in the analysis of 3 group samples of uninfected and 3 of infected mice. Extracts were infused into a 12-T Apex-Qe hybrid quadrupole-FT-ICR mass spectrometer equipped with an Apollo II electrospray ionization source, a quadrupole mass filter and a hexapole collision cell. Raw mass spectrometry data were processed as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140 [PMID 19081807]). To identify differences in metabolite composition between uninfected and infected samples, we filtered the list of masses for metabolites which were present on one set of samples but not the other. Additionally, we calculated the ratios between averaged intensities of metabolites from uninfected and infected mice. To assign possible metabolite identities, monoisotopic neutral masses of interest were queried against MassTrix (http://masstrix.org). Masses were searched against the Mus musculus database within a mass error of 3 ppm. Data were analyzed by unpaired t tests with 95% confidence intervals.

first: L

first: Ellen

last: Arena

first: Alfredo

last: Menendez

middle: B

first: Michelle

last: Buckner


title: MicroRNA Profile Predicts Recurrence of Hepatocellular Carcinoma in Milan Criteria Cases with Mild Liver Cirrhosis.

city: Kyoto

first: Akira

last: Myomoto

address: Yoshida-Shimoadachi

institute: Kyoto Univ.

summary: In this study, we utilized microRNA expression profiling to assess risk of HCC recurrence after liver resection.

overall_design: We examined microRNA expression profiling in paired tumor and non-tumor liver tissues of 73 HCC patients with mild cirrhosis (Child-Pugh A/B) who satisfy Milan Criteria. We constructed prediction models of recurrence-free survival using Cox proportional hazard model and principal component analysis.

first: Fumiaki

last: Sato

first: Etsuro

last: Hatano

first: Koji

last: Kitamura

first: Takeshi

last: Fujiwara

first: Satoko

last: Takizawa

first: Soken

last: Tsuchiya

first: Gozoh

last: Tsujimoto

first: Shinji

last: Uemoto

first: Kazuharu

last: Shimizu


title: [E-MTAB-75] Cryptic unstable transcripts in yeast

status: Public on Feb 05 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

type: Expression profiling by high throughput sequencing

summary:
Poly(A) and CUT RNA fractions are compared using 3 'Long-SAGE deep-sequencing.

ArrayExpress Release Date: 2008-12-19

Publication Title: Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
Publication Author List: Helen Neil, Christophe Malabat, Yves d'Aubenton-Carafa, Zhenyu Xu, Lars M. Steinmetz and Alain Jacquier

Person Roles: submitter
Person Last Name: Malabat
Person First Name: Christophe
Person Mid Initials:
Person Email: christophe.malabat@pasteur.fr
Person Phone:
Person Address: Unité de Génétique des Interactions Macromoléculaires; CNRS, URA2171,F-75015, Paris, France
Person Affiliation: Institut Pasteur

overall_design:
Experimental Design: genetic_modification_design
Experimental Design: reference_design
Experimental Design: high_throughput_sequencing_design
Experimental Factor Name: Genotype
Experimental Factor Name: StrainOrLine
Experimental Factor Type: genotype
Experimental Factor Type: strain_or_line


title: Analysis of the miRNA profile associated with c-Src-mediated transformation

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To address the molecular mechanisms underlying c-Src-mediated tumor progression, we previously developed a model system using Csk-deficient fibroblasts that can be transformed by wild-type c-Src. In this study, we applied this system for the analysis of the potential contribution of miRNA to c-Src-mediated transformation. Pair-wise significance analysis of the microarray indicated that seven miR genes were significantly upregulated and six miRNA genes were downregulated in c-Src-transformed cells with a P value below 0.01 and with a fold change over 2.0.

overall_design: Csk-/- mouse embryonic fibroblasts (Csk-/- MEFs) were transfected with empty vector, c-Src, Csk/c-Src, or Csk. Each sample was run in duplicate.

first: Chitose

last: Oneyama

first: Masato

last: Okada