title: Bobwhite Quail 2,6-DNT

status: Public on Dec 10 2009

city: Hattiesburg

first: Arun

last: Rawat

state: MS

address: 118 College Drive # 5018

department: Biological Sciences

institute: University of Southern Mississippi

summary: Investigating the effects of a subchronic (60d) exposure to the munitions constituent (MC) 2,6-DNT on Northern bobwhite.

overall_design: Gene expression among liver and feather pulp in Northern bobwhite at control, 10 and 60 mg/kg/d doses. 4 replicate for each level.

first: Kurt

last: Gust


title: A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation.

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

summary: Analysis of the intergenic regions of Staphylococcus aureus by bioinformatics predicted multiple regulatory regions. From this analysis, we also characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma factor B (RsaA, D, and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other staphylococci, and RsaE is additionally present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE-mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C-rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism.

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

platform_organism: Staphylococcus aureus subsp. aureus Mu50

platform_organism: Staphylococcus aureus subsp. aureus N315

platform_organism: Staphylococcus aureus subsp. aureus MRSA252

platform_organism: Staphylococcus aureus subsp. aureus MSSA476

platform_organism: Staphylococcus aureus subsp. aureus USA300

overall_design:
Total RNA of the strain Staphylococcus aureus RN6390 (wild type) was co-hybridized in duplicate with the RsaX15 mutant strain (Staphylococcus aureus Lug1430). cDNA of RN6390 was labeled with Cy-5 ; cDNA of RN6390 was labeled with Cy-3.
Hybridization, performed in Agilent proprietary buffer was performed for 17H at 60°C. Slides were then scanned in the Agilent scanner and extracted with Feature Extraction software. Background subtracted data were normalized for unequal incorporation or loading (LOWESS).

first: Thomas

last: Geissmann

first: Clément

last: Chevalier

first: Marie-Josée

last: Cros

first: Sandrine

last: Boisset

first: Pierre

last: Fechter

first: Cécile

last: Noirot

first: Jacques

last: Schrenzel

first: Patrice

last: Francois

first: Francois

last: Vandenesch

first: Christine

last: Gaspin

first: Pascale

last: Romby


title: Transient Genotype-by-Environment Interactions in the Yeast Genomic Expression Response to Heat Shock

status: Public on Dec 15 2009

city: Madison

first: Audrey

middle: P.

last: Gasch

state: WI

address: 425-g Henry Mall

department: Laboratory of Genetics

country: USA

institute: University of Wisconsin Madison

summary:
Microarray time courses followed the response of 5 yeast strains to heat shock.  Expression variation due to genetic, environmental, and genotype-by-environment interactions were identified.

Keywords: Timecourse and single timepoint expression studies of stress response in yeast

overall_design: The genomic expression response to heat shock was measured in 5 different yeast strains over the course of 2 hours. Basal expression at 25C was also compared in 4 non-lab strains to the S288c refernce. All experiments were done in duplicate, for a total of 68 Samples.

first: Kevin

last: Ng

first: Daniel

middle: J

last: Kvitek

first: Sunduz

last: Keles

middle: P


title: Sequence discrimination study

city: New York

first: David

last: Gresham

state: NY

address: 100 Washington Sq East, 1009 Sliver Center

department: Biology

institute: New York University

summary:
The use of DNA microarrays to identify nucleotide variation is almost 20 years old. A variety of improvements in probe design and experimental conditions have brought this technology to the point that single-nucleotide differences can be efficiently detected in unmixed samples, although developing reliable methods for detection of mixed sequences (e.g. heterozygotes) remains challenging. Surprisingly, a comprehensive study of the probe design parameters and experimental conditions that optimize discrimination of single nucleotide polymorphisms (SNPs) has yet to be reported, so the limits of this technology remain uncertain. By targeting 24,549 SNPs that differ between two Saccharomyces cerevisiae strains, we studied the effect of SNPs on hybridization efficiency to DNA microarray probes of different lengths under different hybridization conditions.  We found that the critical parameter for optimization of sequence discrimination is the relationship between probe melting temperature (Tm) and the temperature at which the hybridization reaction is performed.  This relationship can be exploited through the design of microarrays containing probes of equal Tm by varying the length of probes.  We demonstrate that using such a microarray we detect >90% homozygous SNPs and >80% heterozygous SNPs using the SNPScanner algorithm.  The optimized design and experimental parameters determined in this study should guide DNA microarray designs for applications that require sequence discrimination such as mutation detection, genotyping of unmixed and mixed samples and allele-specific gene expression.  Moreover, designing microarray probes with optimized sensitivity to mismatches should increase the accuracy of standard microarray applications such as copy number variation detection and gene expression analysis.

Keyword(s): MutationDetection_CGH

overall_design: Comparison of polymorphic vs non-polymorphic genomes when hybridrized to short probe microarrays

last: Botstein


title: Hepatic gene expression study

city: Stockholm

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

country: Sweden

institute: Karolinska institutet

summary:
The aim of this study was to compare the effects of cocoa butter and safflower oil on hepatic transcript profiles, lipid metabolism and insulin sensitivity in healthy rats. Cocoa butter-based high-fat feeding for three days did not affect plasma total triglyceride (TG) levels or TG-rich VLDL particles or hepatic insulin sensitivity, but changes in hepatic gene expression were induced that might lead to increased lipid synthesis, lipotoxicity, inflammation and insulin resistance if maintained. Safflower oil increased hepatic β-oxidation, was beneficial in terms of circulating TG-rich VLDL particles, but led to reduced hepatic insulin sensitivity. The effects of safflower oil on hepatic gene expression were partly overlapping with those exerted by cocoa butter, but fewer transcripts from anabolic pathways were altered. Increased hepatic cholesterol levels and increased expression of hepatic CYP7A1 and ABCG5 mRNA, important gene products in bile acid production and cholesterol excretion, were specific effects elicited by safflower oil only. Common effects on gene expression included increased levels of p8, DIG-1 IGFBP-1 and FGF21, and reduced levels of SCD-1 and SCD-2. This indicates that a lipid-induced program for hepatic lipid disposal and cell survival was induced by three days of high-fat feeding, independent on the lipid source. Based on the results, we speculate that hepatic TG infiltration leads to reduced expression of SCD-1, which might mediate either neutral, beneficial or unfavourable effects on hepatic metabolism upon high-fat feeding, depending on which fatty acids were provided by the diet.

Keywords: Hepatic gene expression

overall_design: Two-condition experiment. Biological replicates: 4 male rat livers from rats on a standard diet, 4 male rat livers from rats on a cocoa butter diet, 4 male rat livers from rats on a high-fat (safflower oil) diet.  One replicate per array.

middle: E

first: Paolo

last: Parini

first: Jovanka

last: Ostojic

first: Louisa

last: Cheung

first: Jin

last: Hu

first: Fahad

last: Zadjali

first: Faheem

last: Tahir

first: Kerstin

last: Brismar

first: Gunnar

last: Norstedt

first: Petra

last: Tollet-Egnell


title: Higher Order Chromosomal Network of Imprinted Loci

status: Public on Dec 14 2009

first: Rolf

last: Ohlsson

address: Nobels väg 16

department: Microbiology, Tumour and Cell biology

institute: Karolinska Institute

summary: It is increasingly being recognized that physical interactions between distant chromosomal loci influence the expressivity of the genome. Thus, multiple enhancers may converge on a single gene promoter 1,2 and a single enhancer can stochastically loop to multiple promoters 3. Regulatory elements from neighboring domains or from other chromosomes may interact to generate chromatin structures poised for transcription4-8 or repression 9-11. However, a broader perspective on the formation and function of such networks remains largely unexplored. Using the high-resolution 4C (Circular Chromosome Conformation Capture) analysis, we identify here a genome-wide physical network between genomically imprinted domains impinging H19 imprinting control region (ICR). Sequences interacting with the H19 ICR constitutively map at or within most of known imprinted domains both in mouse embryonic stem cells and in vitro-derived embryoid bodies, despite distinct differences in chromatin environments. Moreover, all-to-all 3D DNA FISH analyses revealed that imprinted domains from 7 different chromosomes co-localize with each other in pair-wise patterns, highlighting the dynamic nature of these interactions. The observed interaction network is dependent on CTCF binding sites within the maternally inherited H19 ICR allele and delays reprogramming of epigenetic features at imprinted domains during male germline development. As other imprinted regions can interact with each other in an H19 ICR-dependent manner, the H19 ICR emerges as an organizer of chromosomal networks by specifically recognizing and reconfiguring imprinted domains. We propose that an ancient key regulatory region, such as the H19 ICR, gradually impacted epigenetic modifications via long-range interactions in the germline to facilitate the recruitment of imprinted genes and their formation in clusters during mammalian radiation. Furthermore, the perspective of epigenetic lesions de-stabilizing such chromosomal networks may advance our understanding of how quantitative traits influence human diseases, such as cancer.

overall_design: Circular Chromosome Conformation Capture (4C) experiments were performed on mouse embryonic cell line (R1) and in-vitro derived embryoid bodies taking H19 ICR as a bait. Resulting 4C product and input DNA was hybridized on NimbleGen tiling array dedicated for genomic locations preferred for interactions as determined by a genome-wide 4C screen of pooled samples from neonatal liver, neonatal brain, ES cells and embryoid bodies. The experiments were performed in two distinct biological replicates, each representing a pool of three independent samples.


title: Peri-implantation gestational day 11 porcine embryos

city: Beltsville

first: Le Ann

last: Blomberg

state: MD

address: 10300 Baltimore Ave

department: ANRI

institute: USDA-ARS

summary: Asynchrony of trophectoderm elongation, gestational days 11-12, is evident in porcine concepti and, rapid progression through this phase has been associated with conceptus competency.   The goal of the current study was to determine the extent of transcriptomic responses of concepti to developmental delay and their physiological implications.  Concepti with the same morphology, ovoid and 7-8 mm, were isolated and designated as normal or developmentally delayed if collected from a homogenous ovoid conceptus population or a heterogeneous conceptus population (ovoid to filamentous), respectively.  Total RNA prepared from 4 distinct normal and 4 distinct developmentally delayed concepti, was analyzed using an Agilent high-density custom porcine microarray.  Two hundred-nine transcripts were found differentially expressed between normal and developmentally delayed concepti.  Functional analysis of these genes indicated that a significant number of the genes regulate signal transduction/transcription, organismal development, metabolism, and cell adhesion and can be modulated by transforming growth factor β1.  Ten genes were selected for real-time PCR validation of differential expression based on a known role in steroid synthesis, endometrium receptivity, and modulation of trophoblast differentiation/growth or interaction with transforming growth factor β1.  As in the microarray, all except one, achaete-scute complex homolog 2, were preferentially up-regulated in delayed concepti.  Overall, the findings suggested that developmentally delayed concepti are distinct from their morphologically similar counterparts and more developmentally advanced concepti.  Furthermore, it also highlighted ways by which the conceptus’ microenvironment might be affected and pinpointed developmental factors that can be interrogated further to determine if, and how, they affect embryo competency/elongation.

overall_design:
Gene expression of developmentally delayed day ~ 11.5 ovoid embryos from a heterogeneous embryo population was compared to day 11 ovoid embryos from a homogeneous embryo popluation.  An n of 4 was compared for each group with the embryos from the homogenous population being the control and those from the heterogeneous population the experimental. The interest was to see where morphology or the uterine environment was a better predictor of the transcriptome profile and its implications on the development potential/compentence of the the developmentally delayed embryo.
Self-self hybridizations for control and experimental samples.

first: LeAnn

first: Lori

middle: L

last: Schreier

first: Robert

last: LI


title: Gene regulation by the RcsCB two-component system and the auxiliary protein TviA in S. Typhi

status: Public on Dec 11 2009

city: Davis

first: Sebastian

last: Winter

state: CA

address: One Shields Ave

department: MMI

institute: UC Davis

summary: In response to osmolarity, Salmonella enterica serotype Typhi (S. Typhi) regulates genes required for Vi capsular antigen expression oppositely to those required for motility and invasion. Previous studies suggest that osmoregulation of motility, invasion and capsule expression is mediated through the RcsC/RcsD/RcsB phosphorelay system. Here we performed gene expression profiling and functional studies to determine the role of TviA, an auxiliary protein of the RcsB response regulator, in controlling virulence gene expression in S. Typhi. TviA repressed expression of genes encoding flagella and the invasion associated type III secretion system (T3SS-1) through repression of the flagellar regulators flhDC and fliZ, resulting in reduced invasion and reduced expression of FliC. Both RcsB and TviA reduced expression of flhDC, but only TviA altered flhDC expression in response to osmolarity. These data suggest that the auxiliary TviA protein integrates a new regulatory input into the RcsB regulon of S. Typhi, thereby altering expression of genes encoding flagella, the Vi antigen and T3SS-1 in response to osmolarity.

sample_organism: Salmonella enterica subsp. enterica serovar Typhi

overall_design: Gene expression profiles of the S. Typhi wild-type strain, a rcsB mutant, a  (delta)tviB-vexE (tviBCDEvexABCDE) mutant, and a (delta)viaB (tviABCDEvexABCDE) mutant (lacking tviA expression) was compared. Strains were cultured in SOB broth (low salt), a condition known to induce expression of TviA and the RcsCB system. Total RNA was extracted from two independent cultures (biological replicates) of each strain. cDNA was differentially labeled with Alexa Fluor 555 and 648, respectively and competitively hybridized on S.Typhimurium arrays (PFGRC, version 4). The submitted samples are biological replicates of a competitive hybridization of cDNA from the wild-type strain (Ty2) and the rcsB mutant (SW237) (GSM395580, GSM395581) or the viaB mutant (STY2) and the tviB-vexE mutant (SW74) (GSM395582, GSM395583), respectively.

first: Andreas

last: Baumler


title: Human epithelial cell response to bacterial signal indole

status: Public on Dec 22 2009

city: College Station

first: Tarun

last: Bansal

state: TX

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A & M University

summary:
Indole is a bacterial signal secreted by pathogenic and commensal Escherichia coli in the stationary phase at high concentrations (~600 µM). Prior work from our lab has shown that indole decreases E. coli O157:H7 (EHEC) chemotaxis, motility, attachment to epithelial cells and biofilm formation. However, its effect on epithelial cells is not known. We hypothesized that indole induces gene expression changes in epithelial cells that lead to decreased pathogen colonization and infection. Changes in gene expression with the human enterocyte cell line HCT-8 exposed to indole suggested down-regulation of Toll-like receptor signaling and coordinated changes in Jak-STAT and p38 MAPK pathways. Corresponding changes in the expression of cytokines, chemokines, and their receptors also suggested that indole functions as a modulator of inflammation in intestinal epithelial cells. In addition, the expression of genes involved in tight junction organization (claudins, and tight junction proteins) and mucin production were also up-regulated by indole.

Keywords: Inter-kingdom signaling interactions between human cells and bacterial signal indole

overall_design: Human intestinal epithelial cells were exposed to 1 mM indole for 4 h or 24 h. RNA was isolated from the control cells and cells exposed to indole for 4 h and 24 h. The experiments were performed in triplicate. A total of 9 microarrays were performed, three for each condition. The gene expression data was analyzed using significance analysis of microarrays (SAM) where a false discovery rate cut-off of 1% was used. The genes were then classified and importnat regulated pathways were reported.

first: Thomas

middle: K

last: Wood

first: Arul

last: Jayaraman


title: Expression Profiles of 15(S)-HETE treated RAW 264.7 cells

status: Public on Dec 17 2009

city: Nashville

first: David

middle: W

last: Wright

state: TN

address: SC Stevenson Center 7, Station B 351822

department: Chemistry

institute: Vanderbilt University

summary: Hemozoin phagocytosis results in immunomodulation. This study was designed to explore gene expression responses to 15(S)-HETE in LPS-stimulated RAW 264.7 cells.

overall_design: Three biological replicates were analyzed for each treatment type. Each replicate was composed of 6 pooled wells from a 6-well plate.

first: Alexandra

middle: C

last: Schrimpe


title: mRNA expression profiling of mouse microvasculature

first: Liqun

last: He

address: Scheelesvag 2

summary:
Combination of reverse- and chemical genetic screens reveals a network of novel angiogenesis inhibitors and targets    Drug target identification and validation are bottlenecks in the drug discovery process. Accordingly there is a need to develop new methods to facilitate the development of much-needed innovative drugs. We have combined reverse- and chemical genetics to identify new targets modulating blood vessel development. Through mRNA expression profiling in mice we identified 155 drugable gene products that were enriched in the microvasculature. Orthologs of 50 of these candidates were knocked down in a reverse genetic screen in zebrafish. 16 of the 50 genes encoded products that affected angiogenesis. In parallel, screening of 300 known drugs and pharmacologically active compounds in a human cell-based angiogenesis assay identified 11 angiogenesis inhibitors. Strikingly the reverse- and chemical genetic screens identified an overlap of three gene products of the same superfamily of serine/threonine protein phosphatases and two compounds targeting that family. Furthermore, the gene products identified in the reverse genetic screen comprise an interacting network with the targets of the chemical genetic screen. Thus, combining reverse- and chemical genetic screens is a powerful approach to identify novel biological processes and drug targets in vertebrates.
Keywords: Cell-type comparison

overall_design: 24 samples were analyzed, representing 8 sample groups. In every sample group, three biological replicates were hybridized separately. The microarrays were hybridized with a Cy3-labeled sample and Cy-5 labeled Common Reference (Universal Mouse Reference RNA, cat. No.: 740100, Stratagene) simultaneously.

first: Elisabet

last: Wallgard

first: Mattias

last: Kalen

first: Noomi

last: Asker

first: Aidas

last: Nasevicius

first: Lisa

last: Athley

first: Anna

last: Niemi

first: Erik

last: Billgren

first: Jon

middle: D

last: Larson

first: Shannon

middle: A

last: Wadman

first: Linda

last: Karlsson-Lindahl

first: Ann-Katrin

last: Nilsson

first: Tore

last: Samuelsson

first: Jeffrey

last: Essner

first: Perry

middle: B

last: Hackett

first: Mats

last: Hellström


title: SNP array data of breast cancer

status: Public on Dec 23 2009

city: Boston

first: Zhigang

last: Wang

state: MA

address: 44 Binney St SM936A

department: Cancer Biology

institute: Dana-Farber Cancer Institute

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

summary:
Genome-wide study of LOH and copy number changes associated with breast cancer, their subtypes and their clinical outcome including response to chemotherapy in women sufferred from breast cancinomas.
Mapping chromosome 8q22 copy gain associated with poor clinical outcome of breast cancer and discovery of 8q22 genes relevant to specific drug resistance.

overall_design: Affymetrix GenChip 10K SNP Xba131 arrays were used according to the manufacturer's directions on DNA extracted from breast cancer cells enriched by needle microdissection and from paired peripheral blood samples in 50 breast tumors of high grade. Copy number analysis using dChip software was performed to identify poor outcome-associated chromosomal amplification and to correlate with gene expression.

first: Andrea

last: Richardson


title: microRNA profiling of extraocular muscles

city: Philadelphia

first: Ulrike

last: Zeiger

state: PA

address: 3700 Hamilton Walk

department: Physiology and PMI

institute: University of Pennsylvania

summary: The extraocular muscles (EOMs) are a unique group of muscles that are anatomically and physiologically distinct from other skeletal muscles. Previously, we and others have shown that EOMs have a unique transcriptome and proteome. Here, we investigated the expression pattern of microRNAs (miRNAs) in EOM, as they may play a role in generating the unique EOM allotype. We screened LC Sciences miRNA microarrays covering the sequences of miRBase 10.0 to define the microRNAome of normal mouse EOM and tibialis anterior (TA) limb muscle. 74 miRNAs were found to be differentially regulated (p-value < 0.05) and 31 miRNAs (14 up-regulated and 17 down-regulated) were found to be differentially regulated at a signal strength > 500 including the muscle-specific miR-206, miR-1, miR-133a, miR-133b and miR-499. qPCR analysis was used to validate the differential expression. Bioinformatic tools were used to identify potential miRNA-mRNA-protein interactions and integrate data with previous transcriptome and proteomic profiling data. Luciferase assays using co-transfection of precursor miRNAs (pre-miRNAs) along with reporter constructs containing the 3’-untranslated region (3’UTR) of their predicted target genes were used to validate targeting by identified miRNAs. The definition of the EOM microRNAome complements existing transcriptome and proteome data about the molecular make-up of EOM and provides further insight into regulation of muscle genes. These data will also help to further explain the unique EOM muscle allotype and its differential sensitivity to diseases such as Duchenne's muscular dystrophy (DMD) and may assist in development of therapeutic strategies.

overall_design: Total RNA from four EOM and four TA tissue samples dissected from four adult male C57/Bl10 mice were used (TA served as control) to screen four LC Sciences microRNA Microarray chips. The chips contained microRNA sequences based on miRBase content 10.0 totalling 568 different miRNAs. Samples were labelled with Cy3 and Cy5 using dye-swap. Relative differences of miRNA expression was expressed as fold-changes EOM/TA, which were calculated after normalization across all four arrays.

first: Tejvir

middle: S

last: Khurana


title: Bdellovibrio bacteriovorus infection of E. coli

status: Public on Dec 09 2009

city: Nottingham

first: Carey

last: Lambert

state: Notts

address: Queen's Medical Centre

department: Genetics

country: United Kingdom

institute: Nottingham University

summary:
The transcriptional response of E. coli being predated by Bdellovibrio bacteriovorus
Keywords: Transcriptional analysis

sample_organism:
Escherichia coli
Bdellovibrio bacteriovorus

overall_design:
5 biological replicates with 2 technical replicates each of E. coli cells only and E. coli cells 15 minutes post-infection arrays 4 arrays, with samples swapped for each biological replicate.

Gel image files generated by the ImageQuant scanning software.

Each raw data txt file has the "control" samples which are the E. coli samples reading on the entire array and thus with the 2 technical replicates, and the "data" samples to which it is compared by Arrayvision. the "data" samples of ec1 to ec5 are Bdellovibrio only controls 2 technical replicates). The "data" samples of t1 to t5 are the test samples. Hence t1 to t5 are the raw data files for samples test1 to test10 and ec1 to ec5 are the raw data files for all of samples ec-1 to ec-10 and bd-1 to bd-10.

first: Liz

last: Sockett


title: Melospiza melodia hypothalamus: control and STI in two seasons (spring and autumn)

status: Public on Dec 16 2009

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

institute: University of Illinois

summary: Male song sparrows (Melospiza melodia) are territorial year-round; however, neuroendocrine responses to simulated territorial intrusion (STI) differ between breeding (spring) and non-breeding seasons (autumn).  In spring, exposure to STI leads to increases in luteinizing hormone and testosterone, but not in autumn.  These observations suggest that there are fundamental differences in the mechanisms driving neuroendocrine responses to STI between seasons.  Microarrays, spotted with EST cDNA clones of zebra finch, were used to explore gene expression profiles in the hypothalamus after territorial aggression in two different seasons.  Free-living territorial male song sparrows were exposed to either conspecific or heterospecific (control) males in an STI in spring and autumn.  Behavioral data were recorded, whole hypothalami were collected, and microarray hybridizations were performed.  Quantitative PCR was performed for validation.  Our results show 262 cDNAs were differentially expressed between spring and autumn in the control birds.  There were 173 cDNAs significantly affected by STI in autumn; however, only 67 were significantly affected by STI in spring.  There were 88 cDNAs that showed significant interactions in both season and STI.  Results suggest that STI drives differential genomic responses in the hypothalamus in the spring vs. autumn. The number of cDNAs differentially expressed in relation to season was greater than in relation to social interactions, suggesting major underlying seasonal effects in the hypothalamus which may determine the differential response upon social interaction.  Functional pathway analyses implicated genes that regulate thyroid hormone action and neuroplasticity as targets of this neuroendocrine regulation.

sample_organism:
Melospiza melodia
Taeniopygia guttata

overall_design: For condition experiment, SC (spring control), AC (autumn control), SE (spring STI), AE (autumn STI)  Biological replicates: 7 in SC, 8 in AC, SE, AE. One Melospiza melodia subject and one universal SoNG reference (pooled Taeniopygia guttata brain) per array.

first: John

last: Wingfied

first: Motoko

last: Mukai

first: Jenny

last: Drnevich

first: Gang

first: Douglas

last: Wacker

first: Mark

last: Band

first: David

middle: F

last: Clayton


title: Mycoplasma pneumoniae expression profiling

city: Barcelona

first: Marc

last: Güell

address: C/ Dr.Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

summary:
Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. We have found 68 new non-annotated transcripts, of which the vast majority are potential regulatory RNAs, 53 of them in antisense to known genes. Integration of all data confirmed a dynamic and complex view of bacterial transcription: Under reference conditions in a rich medium, 138 polycistronic and 212 monocistronic transcripts could be identified, with almost half of the polycistronic operons showing a ‘staircase’-like expression pattern, i.e. the expression level within each gene is constant, but succeeding genes have lower expression. Furthermore, under different conditions, operons can divide into smaller transcriptional units, possibly by utilization of internal promoters resulting in many alternative transcripts.  More complex bacteria show similar responses to external stresses, although M. pneumoniae lacks the respective transcription regulators, indicating the existence of yet uncharacterized common response mechanisms. This is supported by the concerted expression of genes, some of which with common upstream DNA motifs, form distinct operons under different conditions indicating additional factors regulating their expression. Frequent antisense transcripts, alternative transcripts and multiple regulators per gene thus cannot longer be seen as indicators of eukaryote-specific regulatory complexity.

Keywords: Stress, genetic modification, time series, drug treatment

overall_design: 252 samples are analyzed including genetic mutants, time series, drug treatment, stress

first: Eva

last: Yus

first: Sabine

last: Schmidt

first: Vladimir

last: Benes

first: Gavin

last: Anne-Claude

first: Luis

last: Serrano


title: In silico enhanced restriction enzyme based methylation analysis of the human glioblastoma genome

status: Public on Dec 08 2009

city: Los Angeles

first: Albert

last: Lai

address: 635 Charles E. Young Drive S NRB1 555C

department: Neurology

institute: UCLA

type: Methylation profiling by genome tiling array

summary: Genome wide methylation profiling of gliomas is likely to provide important clues to improving treatment outcomes. Restriction enzyme based approaches have been widely utilized for methylation profiling of cancer genomes and will continue to have importance in combination with higher density microarrays. With the availability of the human genome sequence and microarray probe sequences, these approaches can be readily characterized and optimized via in silico modeling.  We adapted the previously described HpaII/MspI based Methylation Sensitive Restriction Enzyme (MSRE) assay for use with two-color Agilent 244K CpG island microarrays.  In this assay, fragmented genomic DNA is digested in separate reactions with isoschizomeric HpaII (methylation-sensitive) and MspI (methylation-insensitive) restriction enzymes.  Using in silico hybridization, we found that genomic fragmentation with BfaI was superior to MseI, providing a maximum effective coverage of 22,362 CpG islands in the human genome.  In addition, we confirmed the presence of an internal control group of fragments lacking HpaII/MspI sites which enable separation of methylated and unmethylated fragments.   We used this method on genomic DNA isolated from normal brain, U87MG cells, and a glioblastoma patient tumor sample and confirmed selected differentially methylated CpG islands using bisulfite sequencing.   Along with additional validation points, we performed a receiver operating characteristics (ROC) analysis to determine the optimal threshold (p ≤ 0.001).   Based on this threshold, we identified ~2400 CpG islands common to all three samples and 145 CpG islands unique to glioblastoma.  These data provide general guidance to individuals seeking to maximize effective coverage using restriction enzyme based methylation profiling approaches.

overall_design: Five samples: normal human brain DNA, U87MG cell line, glioblastoma tumor, human DNA treated with SssI enzyme used as positive control, and Genomiphied human DNA used as negative control.  Two technical replicates were performed on all samples except the negative control.

first: Weidong

last: Chen

first: Anh

last: Tran


title: Dynamic cell culture in bubble-confined cell array

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary:
One of the important issues in advanced cell culture development is to create an accurate and controlled micro-environment surrounding the cell while meeting the requirements for processes such as cell differentiation, gene function or pharmacological screening tests. In this sight, we were aimed at designing and developing a micro-scale culture system suitable to analyze the synergic effects of extracellular matrix proteins and soluble environment on cell phenotype in high-throughput fashion. Moreover we were interested in the opportunity to create a more “tissue-friendly” microenvironment than traditional culture methods simulating liquids movements.
According to these purposes, cell arrays were produced deposing micrometer-scale protein islands on polyacrylamide hydrogels using a robotic DNA microarrayer and were used both in conventional culture methods and by automated stable and constant perfusion.
We produced a mathematical modeling assisting the experimental design and assessing efficient mass transport and proper fluidodynamic regimes. It was validated using a particle tracking experiment used to predict the constant value of the velocities over the cell arrays which ensure the same mass transport regime over the cultured cell arrays.
Cell-array permits the maintenance of the correct phenotype of cells cultured on 500 μm islands both in static and dynamic conditions.  Immunostaining and gene expression analysis confirmed the ability for cells to proliferate and differentiate in response to changed stimuli. Microarray gene expression analysis evidenced activation of specific skeletal muscle genes like MYL2, confirmed by qRT-PCR, and troponins and tropomyosins.
Keywords: cell array, dynamic, perfusion, C2C12, hydrogel, ECM

overall_design:
C2C12 cells were cultured onto the protein microarray specifically produced. Cells were cultured in a dynamic flow medium. After 6 and 24 hours in proliferative medium and 24 and 60 hours in differentiative medium total RNA was extracted and used to perform linear amplification and microarray and qRT-PCR gene expression experiments. Cells cultured for 24 hours in proliferative medium and in confluence state were used as common control in all experiments. At least 2 microarray experiments were performed for each time point (technical replicate).
Each slide was scanned and extracted data was normalized and analyzed. Data were used for clustering genes and experiments analysis.

Series table "Experiment filtering details" pertains to the data filtering steps in the Sample 'Data processing' fields.

first: Elisa

last: Cimetta

first: Stefano

last: Cagnin

first: Annamaria

last: Volpatti

first: Nicola

last: Elvassore


title: Inhibition of dendritic cell maturation and effector function

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

summary:
The initiation of donor derived dendritic cell (DC) adhesion and migration are one of the key events mediated by ischemia reperfusion injury (IRI) following solid organ transplantation. Recently we have been able to demonstrate that a single donor treatment with the synthetic metalloporphyrin cobalt protoporphyrin (CoPPIX) for heme oxygenase 1 (HO-1) induction results in the reduction of donor-derived DCs following IRI thus leading to the preservation of graft long-term function. Gene expression analysis in murine liver revealed the up-regulation of the signal transducer and activator of transcription 3 (STAT3) after CoPPIX treatment. Since it has been shown that CoPPIX is able to inhibit DC maturation, we could demonstrate that DC (-LPS) induced maturation guided by the secretion of pro-inflammatory cytokines and alloreactive T cell proliferation is dependent of STAT3 phosphorylation and independent of HO-1 activity. These observations highlight the immunomodulatory capacity of STAT3 which might be of further interest for the inhibition of immune response.
Keywords: dendritic cells, heme oxygenase-1 (HO-1), STAT3, cobalt protoporphyrin

overall_design: For the analysis of gene expression profiles in vivo C57BL/6 mice were treated either with 5 mg/kg CoPPIX, i.p.,  50 mg/kg MC, p.o. and 500 ppm CO for 6 or 24 hrs (3 animals in each group). Untreated C57BL/6 mice were used as controls (n=9). After 6 or 24 hrs of treatment animals were sacrificed and whole livers were harvested for analysis.

first: Mir-Farzin

last: Mashreghi

first: Roman

last: Klemz

first: Isabella

last: Schmitt Knosalla

first: Bernhard

last: Gerstmayer

first: Alicja

last: Józkowicz

first: Józef

last: Dulak

first: Roland

last: Buelow

first: Hans-Dieter

last: Volk

first: Katja

last: Kotsch


title: Disruption of PPARg signaling results in mouse prostatic intraepithelial neoplasia (mPIN) involving active autophagy

status: Public on Dec 07 2009

first: Simon

last: Hayward

department: Urologic Surgery

institute: Vanderbilt University Medical Center

summary: Peroxisome proliferator-activated receptor-gamma (PPARg) regulates the interface between cellular lipid metabolism, redox status and organelle differentiation. Following conditional prostatic epithelial knockout of PPARg in mice we observed focal hyperplasia of the epithelium which developed to mouse prostatic intraepithelial neoplasia (mPIN), becoming progressively more severe with time. We selectively knocked down PPARg2 isoform in wild-type mouse prostatic epithelial cells and examined the consequences of this in a tissue recombination model. Histopathologically the results resembled the conditional PPARg KO mouse prostates. Electron microscopy showed accumulated defective lysosomes and autophagic vacuoles in both of PPARg- and g2- deficient cells. Gene expression profiling indicated a major dysregulation of cell cycle control and metabolic signaling networks related to peroxisomal and lysosomal maturation, lipid oxidation and degradation. We conclude that PPARg maintains the maturation and turnover of peroxisomes and lysosomes in prostate epithelium. Disruption of PPARg signaling results in autophagy and oxidative stress during mPIN pathogenesis.

overall_design: The mPrE-PPARg knockout and mPrE-PPARg2 shRNA cells were compared to wildtype mPrE cells. Time (3 days culture) and cell types (x 4) were tested.

first: Ming

last: Jiang

first: Suzanne

last: Fernandez

first: W.

middle: G

last: Jerome

first: Yue

last: He

first: Xiuping

last: Yu

first: Hui

last: Cai

first: Braden

last: Boone

first: Yajun

last: Yi

first: Mark

last: Magnuson

first: Pradip

last: Roy-Burman

first: Robert

last: Matusik

first: Scott

last: Shappell


title: Macrophages stimulated with LPS and Poly (I:C)

first: Joan

last: Balasch

address: UAB Bellaterra faculty of Biosciences

department: Dpt. Cell Biology, Physiology and Immunology

institute: Universitat Autonoma Barcelona

summary: The aim of the current study was to investigate the response of in vitro differentiated trout macrophages, a primary cell culture system widely used in fish immunology research, to lipopolysaccharide (LPS) and to the analog viral ds(RNA) Poly I:C. To that end we have used a salmonid-specific microarray platform enriched with immune-related genes. The results clearly suggest that the molecular mechanisms involved in the response of macrophages to LPS and Poly (I:C) are specific in some signaling pathways related to cell communication, signal transduction and kinase cascades. Nevertheless, macrophages stimulated with bacterial or viral PAMPs also activate common transcription factors.

overall_design:
Trout macrophages were isolated using the protocol previously described
Head kidneys were dissected, placed in sterile 100 µm nylon mesh cell-strainers and homogenized in the presence of DMEM (PAA Laboratories) containing high glucose, 10% heat inactivated FCS (PAA Laboratories) and Primocin antibiotic (100 µg/ml, Invivogen). The homogenates were plated on 60 mm poly-D-lysine (Sigma) treated cell culture Petri plates, 3 ml per plate. The cultures were kept in an incubator at 16 º C and 5% CO2. Non-adhering cells were removed after 24 hours and new medium was added, then adherent cells were incubated for another 4 days. After 5 total days of culture, medium was removed and test cells were stimulated adding
fresh medium containing 10 µg/ml of  LPS from E. coli (serotype 026:B6, Sigma) or 10 µg/ml of Poly (I:C) (Invivogen), whereas medium free of stimulant was added in control plates. All culture plates were incubated for 12h. Six independent experiments (six different fish) were performed for each condition.
Total RNA was extracted from the cultures using 1 ml of Tri Reagent (Sigma), following the manufacturer’s instructions and quantity and integrity was analyzed by Experion RNA StdSens Analysis Kit (Bio-Rad). The design of the microarray posses 1818 genes printed in six replicates each, including random clones from common and subtracted cDNA libraries which were compared with known vertebrate proteins using blastx. The platform was enriched in immune-related genes.

first: Carmen

last: Doñate

last: MacKenzie


title: Bdellovibrio bacteriovorus attack phase and Host-Independent grown cells

first: Carey

last: Lambert

summary: Bdellovibrio is a Gram-negative bacterium that preys upon other Gram-negative bacteria, including many pathogens, and as such has potential as a biocontrol agent. Little is known of the molecular and genetic control of Bdellovibrio’s attack upon its prey and of the nature of the HI phenotype. Here, we apply microarray technology to monitor changes of gene expression during the initial stages of prey infection to determine which predatory genes are important in this stage and to gain insight into possible regulatory mechanisms controlling the predation process. Comparison to gene expression during HI growth reveals a “predatosome” of genes specifically upregulated during predation and implicates some of those important in HI growth.

overall_design: 3 replicates of attack phase cells and 3 replicates of Host-Independent grown cells were analysed on individual arrays.

first: Liz

last: Sockett


title: Mycoplasma pneumoniae transcriptome analysis

first: Marc

last: Güell

type: Expression profiling by genome tiling array

type: Non-coding RNA profiling by genome tiling array

summary:
Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. We have found 68 new non-annotated transcripts, of which the vast majority are potential regulatory RNAs, 53 of them in antisense to known genes. Integration of all data confirmed a dynamic and complex view of bacterial transcription: Under reference conditions in a rich medium, 138 polycistronic and 212 monocistronic transcripts could be identified, with almost half of the polycistronic operons showing a ‘staircase’-like expression pattern, i.e. the expression level within each gene is constant, but succeeding genes have lower expression. Furthermore, under different conditions, operons can divide into smaller transcriptional units, possibly by utilization of internal promoters resulting in many alternative transcripts.  More complex bacteria show similar responses to external stresses, although M. pneumoniae lacks the respective transcription regulators, indicating the existence of yet uncharacterized common response mechanisms. This is supported by the concerted expression of genes, some of which with common upstream DNA motifs, form distinct operons under different conditions indicating additional factors regulating their expression. Frequent antisense transcripts, alternative transcripts and multiple regulators per gene thus cannot longer be seen as indicators of eukaryote-specific regulatory complexity.

Keywords: stress response, time series

overall_design: Transcriptome of M.pneumoniae has been mapped at a 8 bases resolution using a tiling array. Three time series have been included in order to map the dynamic behavior of the transcriptome. Includes replicates from the reference condition.

first: Eva

last: Yus

first: Tomi

last: Bähr-Ivacevic

first: Vladimir

last: Benes

first: Gavin

last: Anne-Claude

first: Luis

last: Serrano


title: microRNA expression in lung tumors of viny-carbamate treated and viny-carbamate and indole-3-carbinol treated mice

status: Public on Dec 06 2009

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

summary:
We examined the differential expression of miRNAs in vinyl carbamate (VC)-induced lung tumors in A/J mice and assessed if the chemopreventive agent indole-3-carbinol (I3C) reversed the effects of the carcinogen. Microarray studies revealed some up-regulated microRNAs, but down-regulation of several microRNAs in carcinogen-treated mice relative to vehicle-treated mice.

Keywords: Expression

sample_organism:
Homo sapiens
Mus musculus

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

overall_design: micro and control RNA from control treated (3 replicates), vinyl carbamate treated (4 replicates) and vinyl carbamate and indole-3-carbinol treated mice was hybridized versus synthetic human DNA to a custom multi-organism oligonucleotide array.

first: Yan

last: Zeng

first: Tamene

last: Melkamu

first: Jiankang

last: Tan

first: Fekadu

last: Kassie


title: Biological indicators of prognosis in Ewing's sarcoma: An emerging role for LGALS3BP

city: Bologna

first: Katia

last: Scotlandi

address: Via di Barbiano 1/10

institute: Istituto Ortopedico Rizzoli

summary:
We create an experimental model of EWS cells that are chemoresistant and unable to give metastasis in mice and identify a molecular signature of potential prognostic value in EWS patients

Keywords: cell type comparison

overall_design: we analyzed 4 EWS cell variants derived from TC-71 cell line with similar phenotype (MDR expression and no ability to form metastasis). Control is the parental cell line TC-71. Cells were profiled with Agilent Human 1 cDNA microarray kit (G4100A)

first: D

last: Zambelli

first: M

last: Zuntini

first: F

last: Nardi

last: Manara

last: Serra

first: L

last: Landuzzi

first: P

last: Lollini

first: S

last: Ferrari

last: Alberghini

first: A

last: Llombart-Bosch

first: E

last: Piccolo

last: Iacobelli

last: Picci

first: K


title: Tamoxifen-resistant human breast cancer cell lines

city: Rotterdam

first: Lambert

last: Dorssers

department: Josephine Nefkens Institute

country: Netherlands

institute: Erasmus MC- University Medical Center Rotterdam

summary:
A functional genetic screen to identify genes causing tamoxifen resistance in an estrogen-dependent human breast cancer cell model was performed. By insertion of defective retrovirus into the genome, individual genetic changes were introduced at random in ZR-75-1 cells. Subsequently, infected cells were selected for their ability to proliferate while being exposed to tamoxifen, and from these cultures stable cell lines were established. The retrovirus insertion sites were mapped enabling the identification of several candidate breast cancer anti-estrogen resistance (BCAR) genes. By cDNA transfection of estrogen-dependent cells resulting in their transformation into a tamoxifen-resistant phenotype, proof was provided for the causative role of BCAR genes.A functional genetic screen to identify genes causing tamoxifen resistance in an estrogen-dependent human breast cancer cell model was performed. By insertion of defective retrovirus into the genome, individual genetic changes were introduced at random in ZR-75-1 cells. Subsequently, infected cells were selected for their ability to proliferate while being exposed to tamoxifen, and from these cultures stable cell lines were established. The retrovirus insertion sites were mapped enabling the identification of several candidate breast cancer anti-estrogen resistance (BCAR) genes identified. By cDNA transfection of estrogen-dependent cells resulting in their transformation into a tamoxifen-resistant phenotype, proof was provided for the causative role of BCAR genes (Van Agthoven et al, Breast Cancer Res Treat DOI:10.1007/s10549-008-9969-5, 2008).
To elucidate the mechanisms how these individual BCAR genes induce cell proliferation in growth-arrested ZR-75-1 cells, we assessed the gene expression patterns between the different groups of cell lines.

Keywords: Expression profiling, reference design

overall_design: RNA was isolated from two independent cultures of 69 tamoxifen-resistant cell lines. Detailed information regarding these cell lines with respect to the viral integration sites, was described previously (Van Agthoven et al, Breast Cancer Res Treat DOI:10.1007/s10549-008-9969-5, 2008). Each sample was hybridized in duplicate/triplicate and once in a dye-swap. The mixture of cell lines used as a reference was detailed previously (Jansen et al, J Clin Oncol 23, 732, 2005).


title: Transcriptome analysis of rice (Oryza sativa cv.TW16) in relation to infection with rice tungro spherical virus (RTSV)

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

summary:
Rice tungro disease is caused by the interaction between Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Infection with RTSV alone does not result in any distinctive symptoms in TW16 that is one of RTSV resistant indica rice. To elucidate the basis of asymptomatic response of rice to RTSV at the gene expression level, global gene response in RTSV-infected TN1 was detected by custom microarray.

Keywords: time course, virus infection, disease response

overall_design: Comparison between RTSV and mock infected rice. Biological replicates: 3 control (mock), 3 RTSV-infected at each time point, independently grown and harvested at 6 to 15 days after inoculation (DAI). 1 samples prepared with whole plant 5 cm above ground and pooled from 5 plants grown under same conditons.

first: Hiroaki

last: Kondoh

first: Setsuko

last: Kimura

first: Teresa

last: De Leon

first: Il-Ryong

last: Choi

first: Shoshi

last: Kikuchi


title: Transcriptome analysis of rice (Oryza sativa cv. Taichung Native 1) in relation to infection with RTSV

summary:
Rice tungro disease is caused by the interaction between Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Infection with RTSV alone does not result in any distinctive symptoms in Taichung Native 1 (TN1) that is one of RTSV susceptive indica rice cultivar. To elucidate the basis of asymptomatic response of rice to RTSV at the gene expression level, global gene response in RTSV-infected TN1 was detected by custom microarray.

Keywords: time course, virus infection, disease response


title: H. ducreyi 35000HP grown in the presence or absence of FCS

status: Public on Dec 05 2009

city: Dallas

first: Eric

last: Hansen

address: 5323 Harry Hines Blvd

department: Microbiology

institute: University of Texas Southwestern Medical Center

summary: Haemophilus ducreyi 35000HP was subjected to different in vitro growth conditions that resemble the in vivo host environment (presence of serum), in order to ascertain the overall changes in gene expression.  This information might identify genes important for colonization and/or survival inside the host.

overall_design: H. ducreyi 35000HP was grown for 8 hours in Columbia broth in the presence or absence of FCS.  After 8 hours total RNA was isolated and processed for DNA microarray analysis. This study includes four biological replicates (paired samples of bacteria grown in the presence/absence of FCS), one of which (Rep1) was selected for dye swap.

first: Maria

last: Labandeira-Rey


title: The effect of sfh deletion on Salmonella Typhimurium gene expression

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

summary: Transcriptional profiling of Salmonella Typhimurium strains SL1344 (pSfR27) and SL1344 (pSfR27) delta sfh to identify 'Sfh-dependent' transcripts

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Two condition experiment in which the transcriptomes of wild-type SL1344 (pSfR27) and SL1344 (pSfR27) delta sfh were compared to identify 'Sfh-dependent' transcripts

first: Andrew

last: Cameron

first: Karsten

last: Hokamp

first: Sacha

last: Lucchini

first: Jay

last: Hinton

first: Charles

last: Dorman


title: Chip-chip from Jurkat with p300 and pol II

status: Public on Dec 04 2009

city: Bethesda

first: Jung

last: Byun

address: 37 convent drive, Bldg 37,  Rm 1042

institute: NCI/NIH

type: Genome binding/occupancy profiling by array

summary:
We profiled the dynamic interaction of p300 with proximal promoters of human T cells identified a class of genes that rapidly coassemble p300 and RNA polymerase II following mitogen stimulation.
We classified the genes that rapidly coassemble p300 and pol II following mitogen stimulation

overall_design: Comparison the unstimulated to  P/I stimulated pol II and p300 enrichment fold in Jurkat

first: Kevin

last: Gardner


title: Microarray Analysis of Temperature-induced Transcriptome of Streptococcus suis serotype 2

status: Public on Dec 02 2009

city: Beijing

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

country: China

institute: Institute of Microbiology and Epidemiology

summary: Streptococcus suis serotype 2 (SS2) is able to cause human infections ranging from superficial wounded skin infections to severe invasive infections such as meningitis and streptococcal toxic shock-like syndrome (STSLS). During its infection cycle, SS2 must acclimatize itself to temperature shift. Herein, a whole-genome DNA microarray was used to investigate the global transcriptional regulation of an invasive SS2 strain grown to late-exponential phase at 29 or 40°C relative to 37°C. The detecting differentially regulated genes included those encoding virulence factors, antigenic proteins, ABC transporters and unknown functions. Our data provided a global profile of gene transcription induced by temperature alteration and shed light on some unforeseen lines for further pathogenesis investigation.

overall_design: A cDNA microarray imprinted with 2156 genes representing about 98% of Streptococcus suis serotype 2 genome was used for transcriptome analysis . For two-sample (reference vs. test) microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation . Accordingly, for each time point, four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides, respectively. Pairwise comparisons were made using dye swaps to avoid labeling bias. A ratio of mRNA levels (test/reference) was calculated for each gene. Significant changes of gene expression were identified with the SAM software . After the SAM analysis, only genes with at least 2-fold changes in expression were collected for further analysis.

first: Zeng

last: Xiaotao

first: Yuan

last: Yuan

first: Wei

last: Yan

first: Jiang

last: Hua

first: Zheng

last: Yuling

first: Yang

last: Ruifu

first: Zhou

last: Dongsheng

last: Yongqiang


title: Differential Expression of MicroRNAs in Mouse Liver under Aberrant Energy Metabolic Status

city: Hangzhou

first: Shengjie

last: Li

address: 79 Qingchun Road

institute: the First Affiliated Hospital of Zhejiang University School of Medicine

summary:
Despite years of effort, exact pathogenesis of non-alcoholic fatty liver disease (NAFLD) remains obscure. To gain an insight into the regulatory roles of microRNAs (miRNAs) in aberrant energy metabolic status and pathogenesis of NAFLD, we analyzed the expression of miRNAs in livers of ob/ob mice, streptozotocin (STZ)-induced type 1 diabetic mice and normal C57BL/6 mice by miRNA microarray. Compared to normal C57BL/6 mice, ob/ob mice showed up-regulation of 8 miRNAs and down-regulation of 4 miRNAs in fatty livers. Up-regulation of miR-34a and down-regulation of miR-122 was found in livers of STZ-induced diabetic mice. These results demonstrate that distinct miRNAs are strongly dysregulated in NAFLD and hyperglycemia. Comparison between miRNA expressions in livers of ob/ob mice and STZ-administered mice further revealed up-regulation of 4 miRNAs and down-regulation of 2 miRNAs in livers of ob/ob mice, indicating that these miRNAs may represent a molecular signature of NAFLD. A distinctive miRNA expression pattern was identified in ob/ob mouse liver and hierarchical clustering of this pattern could clearly discriminate ob/ob mice from either normal C57BL/6 mice or STZ-administered mice. These findings suggest an important role of miRNAs in hepatic energy metabolism and implicate the participation of miRNAs in the pathophysiological processes of NAFLD.

Keywords: disease state analysis

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the present study, we analyzed the expression of miRNAs in livers of 10 ob/ob mice, 8 streptozotocin (STZ)-induced type 1 diabetic mice and 8 normal control C57BL/6 mice by miRNA microarray.

first: Xi

last: Chen

first: Ke

last: Zen

first: Youming

first: Cheng-Yu

last: Zhang


title: CGH data from 58 bladder tumors

status: Public on Dec 01 2009

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

type: Genome variation profiling by genome tiling array

summary:
We present the first computational approach to reconstruct the sequence of copy number alterations driving carcinogenesis from the analysis of several tumor samples of a same patient. Applied to BAC array-CGH and SNP array data from bladder and breast cancers, this method proved highly valuable to establish the clonal relationships between primary tumors and recurrences and to identify the chromosome aberrations at the initiation of tumorigenesis.

Keywords: Comparative Genomic Hybridization

overall_design: An algorithm was developed to reconstruct tumors lineage and the sequence of copy number alterations along tumorigenesis from the analysis of several samples from a same patient. The data here consist in CGH data from 58 bladder tumors. 50 of these tumors come from independent samples and were used to compute the frequencies of breakpoints at each location. The 8 other samples (S1_A, S1_B, S2_A, S2_B, S3_A, S3_B, S3_C and S3_D) are multiple tumors from 3 patients. They were used to reconstruct the sequence of chromosome aberrations along cancer development in these 3 patients.

first: Yves

last: Allory

first: Daniel

last: Pinkel

first: François

last: Radvanyi

first: Nicolas

last: Stranksky


title: A protein microarray-based analysis of S-nitrosylation

city: Durham

first: Matthew

last: Foster

state: NC

address: Box 2612 Research Dr.

department: Medicine

institute: Duke University

summary: Yeast protein microarrays were utilized to investigate determinants of S-nitrosylation by biologically relevant low-mass S-nitrosothiols (SNOs). Large numbers of S-nitrosylated yeast proteins were identified after treatment with SNOs, among which those with active-site Cys thiols residing at N termini of alpha-helices or within catalytic loops were particularly prominent. However, S-nitrosylation varied substantially even within these families of proteins (e.g., papain-related Cys-dependent hydrolases and rhodanese/Cdc25 phosphatases), suggesting that neither secondary structure nor intrinsic nucleophilicity of Cys thiols was sufficient to explain specificity. Further analyses revealed a substantial influence of NO-donor stereochemistry and structure on efficiency of S-nitrosylation as well as an unanticipated and important role for allosteric effectors. Thus, high-throughput screening and unbiased proteome coverage reveal multifactorial determinants of S-nitrosylation (which may be overlooked in alternative proteomic analyses), and support the idea that target specificity can be achieved through rational design of S-nitrosothiols

overall_design: Invitrogen yeast Protoarrays for kinase substrate identification (KSI) were treated with S-nitrosothiols and assayed for protein S-nitrosylation by using a modified biotin switch protocol. Slides were scanned and with a Genepix 4000b scanner (Molecular Devices) using Genepix Pro and analyzed by using Prospector Analyzer (Invitrogen). Results were validated using yeast cell lysates and recombinant, purified yeast proteins.

first: Michael

middle: T

last: Forrester

first: Jonathan

last: Stamler


title: Transcriptome analysis of Bacillus subtilis salt stress adaptation

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

summary: Whole-genome microarray technology and state-of-the-art proteomic techniques were applied to provide a global and time-resolved picture of the physiological response of B. subtilis cells exposed to a severe and sudden osmotic up-shift. This combined experimental approach provided quantitative data for 3961 mRNA profiles, 590 expression profiles of proteins detected in the cytosol and 383 expression profiles of proteins detected in the membrane fraction. Our study uncovered a well-coordinated induction of gene expression subsequent to an osmotic up-shift that involves large parts of the SigB, SigW, SigM and SigX regulons and additionally osmotic up-regulation of a large number of genes that do not belong to these regulons. In total, osmotic up-regulation of about 500 B. subtilis genes was observed. Our data provide an unprecedented rich basis for further in-depth investigation on the physiological and genetic responses of B. subtilis to hyperosmotic stress.

overall_design:
Cells were grown in a minimal medium to early exponential phase and were then exposed to a strong osmotic up-shift by the addition of 6% (w/v) NaCl. Samples were taken before and 10, 30, 60 and 120 min subsequent to the addition of NaCl.
Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool consisting of equal amounts of RNA from all 15 samples was labeled with Cy3 (common reference design).
After intensity-dependent (Lowess) normalization, the ratios of duplicate spots were averaged resulting in three biologically independent expression values per gene and time point.

first: Hannes

last: Hahne

first: Andreas

last: Otto

first: Florian

last: Bonn

first: Leif

last: Steil

first: Erhard

last: Bremer

last: Hecker

first: Dörte

last: Becher


title: Identification of the major PEP-phosphotransferase systems (PTS) for glucose, mannose and cellobiose of L. monocytogenes

city: Würzburg

first: Regina

last: Stoll

address: Biozentrum, Am Hubland

institute: Lehrstuhl für Mikrobiologie

summary:
Identification of the major PEP-phosphotransferase systems (PTS) for glucose, mannose and cellobiose of Listeria monocytogenes, and their significance for extra- and intracellular growth.
Transcriptional profile of prfA, the dependent genes and the PTS genes after growth in MM (minimal medium (Premaratne et al. 2001))  (supplemented with 10 mM Glucose).
Listeria monocytogenes EGD-e possesses 86 pts genes encoding 29 complete and several incomplete PEP-dependent phosphotransferase systems (PTS) for the transport of carbohydrates and sugar alcohols. By a systematic deletion analysis we identified the major PTS involved in glucose, mannose and cellobiose transport, when L. monocytogenes grows in a defined minimal medium in the presence of either of these carbohydrates. Under these conditions two of the four PTSMan and at least one of the five PTSGlc function as glucose transporter with different affinities. Cellobiose is transported (with different efficiencies) mainly by two of the six PTSLac and by a PTSGlc that also transports glucose. One of the PTSMan and both PTSLac are regulated by LevR-homologous PRD containing transcriptional activators, detected with PRD deletion mutants. The growth rates of mutants that are lacking these PTS are drastically reduced compared to the wild-type strain upon growth in a defined medium with low concentrations of glucose and cellobiose, respectively. In contrast, replication of these PTS mutants within epithelial cells or macrophages is as efficient as that of the wild-type strain.

Keywords: pts and prd deletion mutants

overall_design:
A total of three independently isolated RNA samples from each condition were used for the analysis.
PTS Samples: GSM458191-GSM458208
PRD Samples: GSM458209-GSM458214

first: Werner

last: Goebel


title: P. falciparum Histone Occupancy Mapping

city: La Jolla

first: Elizabeth

middle: Ann

last: Winzeler

address: 9500 Gilman Drive 0741

department: Pediatrics

institute: University of California San Diego

type: Genome binding/occupancy profiling by genome tiling array

summary:
Background: Epigenetic modifications of histones and regulation of chromatin structure have been implicated in regulation of virulence gene families in P. falciparum. To better understand chromatin-mediated gene regulation, we used a high-density oligonucleotide microarray to map the position and enrichment of nucleosomes across the entire genome of P. falciparum at three time points of the intra-erythrocytic developmental cycle (IDC) in vitro. We used an unmodified histone H4 antibody for chromatin immunoprecipitation of nucleosome-bound DNA.

Results: We observed generally low nucleosomal occupancy of intergenic regions and higher occupancy of protein coding regions. In contract to the overall small fluctuation of nucleosomal occupancy in most coding regions throughout the IDC, subtelomeric genes encoding surface proteins such as var and rif, as well as some core chromosomal genes such as transcription factors, showed large changes in chromatin structure. Telomeres harbored a region with the highest nucleosomal occupancy of the genome and also exhibited large changes with higher nucleosomal occupancy at schizont stages. While many of these subtelomeric genes were previously shown to be modified by H3K9 trimethylation, we also identified some housekeeping genes in core chromosome regions that showed extensive changes in chromatin structure but do not contain this modification. tRNA and basal transcription factor genes showed low nucleosomal occupancy at all times, suggesting of an open chromatin structure that might be permissive for constitutively high levels of expression. Generally, nucleosomal occupancy was not correlated with the steady-state mRNA levels. Several var genes were exceptions: the var gene with the highest expression level showed the lowest nucleosomal occupancy, and selection of parasites for var2CSA expression resulted in lower nucleosomal occupancy at the var2CSA locus.  We identified nucleosome-free regions in intergenic regions that may serve as transcription start sites or transcription factor binding sites. Using the nucleosomal occupancy data as the baseline, we further mapped the genome-wide enrichment of H3K9 acetylation and detected general enrichment of this mark in intergenic regions.

Conclusions: These data on nucleosome enrichment changes add to our understanding of the influence of chromatin structure on the regulation of gene expression. Histones are generally enriched in coding regions, and relatively poor in intergenic regions. Histone enrichment patterns allow for identification of new putative gene-coding regions. Most genes do not show correlation between chromatin structure and steady-state mRNA levels, indicating the dominant roles of other regulatory mechanisms. We present a genome-wide nucleosomal occupancy map, which can be used as a reference for future experiments of histone modification mapping.

overall_design: Three ChIP with unmodified histone H4 antibodies were performed on ring, trophozoite and schizont stage synchronized parasites. Only one experiment was performed per time point. H3K9ac antibody ChIP was performed on trophozoite stage cells. All samples were normalized to 3D7 strain genomic DNA hybridizations.


title: Grape miRNAs expression profiling in different organs.

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

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

summary: MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. Their action is generally mediated through complementary interactions with mRNA molecules - leading to their degradation or sequestration from the translational apparatus. The recent annotation of the genome of the grapevine Vitis vinifera allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families. Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of smallRNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic cordinates of primary microRNA transcripts, a critical first step towards the elucidation of specific mechanisms regulating the expression of microRNAs at the transcriptional level.

overall_design: Six grapevine (V. vinifera L. cv Corvina) tissues were analyzed: ripening berries (three stages analyzed), roots, leaves and young inflorescences. Each hybridization and LMW-RNA extraction was performed twice. One color labeling was performed.

first: Erica

last: Mica

first: Viviana

last: Piccolo

first: Massimo

last: Delledonne

first: Mario

last: Pezzotti

first: Cesare

last: Casati

first: Cristian

last: Del Fabbro

first: Giorgio

last: Valle

last: Policriti

first: Michele

last: Morgante

first: Graziano

last: Pesole

first: Enrico

middle: M

last: Pè

first: David

last: Horner


title: Pilot application of hepatic cDNA microarray of the sentinel fish striped sea bream as environmental biomarker

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

country: Israel

institute: Israel Oceanographic and Limnological Research

summary:
Feral organisms are affected by adverse environmental factors present in their habitat. It was hypothesized that transcript expression pattern in a suitable target organ of a sentinel feral organism compared to a reference transcript population may serve as a comprehensive biomarker of these adverse effects. This study was aimed at inquiring the applicability of such biomarker and establishing a procedure for its appropriate utilization. The examined system contains dual-labeled microarray-based evaluation of the hepatic transcript expression pattern in a sentinel fish sampled in two habitats, a polluted (Haifa Bay) and a clean (Dor) site, respectively, for two years. The hepatic expression patterns were compared to a reference RNA assumed to represent specimens that have no exposure history to pollution. The sentinel fish is Lithognathus mormyrus, which inhabits a marine coastal habitat along the Mediterranean coast of Israel. The hepatic transcript expression patterns were evaluated using a 1152-clone cDNA microarray, biased towards pollution-affected genes. The LIMMA software was used to calculate the log2 ratios of expressions (M) and to identify the differentially expressed genes in each sample (adjusted P<0.01).

Keywords: Response of fish hepatic gene expression pattern to environmental conditions.

overall_design: Fish were sampled at each of two sites each year. All fish were hybridized to a common reference RNA population using a dye swap design. Hence, each fish was hybridized twice vs the reference RNA. The hybridization results were reanalysed by LIMMA using new division to samples.

first: Yana

last: Yudkovski

first: Meirav

last: Auslander


title: Generation of transcriptome catalogs for global analysis of gene expression in non-model organisms

summary: We have developed a method based on 454 sequencing of 3’ cDNA fragments from a normalized library constructed from pooled RNAs to generate, through de novo reads assembly, a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence, is not available. This “virtual transcriptome” provides extensive coverage depth, and can be used for the set up of a comprehensive microarray based expression analysis. We evaluated the potential of this approach by monitoring gene expression during berry maturation in Vitis vinifera. The microarray designed on the berries’ transcriptome derived from half of a 454 run detected the expression of 19,609 genes, and proven to be more informative than one of the most comprehensive grape microarrays available to date, the GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization, which could detect the expression of 15,556 genes.

overall_design: Microarray oligo probes were designed based on 454 sequencing of 3'-ends of transcripts of a sample constituted by pooling RNAs from grape berries at 6 time points from veraison to whitering. The array was used to analyze the same pool and results were compared to GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization.

first: Diana

last: Bellin

first: Antonio

last: Chimento


title: Modulation of brain dead induced inflammation by vagus nerve stimulation

city: Mannheim

first: Benito

last: Yard

address: Theodor-Kutzer-Ufer 1-3

institute: University hospital Mannheim

summary:
Because the vagus nerve is implicated in control of inflammation, we investigated if brain death causes impairment of the parasympathetic nervous system, hence contributing to inflammation.
Brain death (BD) was induced in rats. Anaesthetised ventilated rats (NBD) served as control. Heart rate variability (HRV) was assessed by ECG. The vagus nerve was electrically stimulated (BD+STIM) during BD. Intestine, kidney, heart and liver were harvested after 6h. Affymetrix chip- analysis was performed on intestinal RNA. Quantitative PCR was performed on all organs. Serum was collected to assess TNFα concentrations. Renal transplantations were performed to address the influence of vagus nerve stimulation on graft outcome.
HRV was significantly lower in BD animals. Vagus nerve stimulation inhibited the increase in serum TNFα concentrations and resulted in down-regulation of a multiplicity of pro-inflammatory genes in intestinal tissue. In renal tissue vagal stimulation significantly decreased the expression of E-selectin, IL1β and ITGA6. Renal function was significantly better in recipients that received a graft from a BD+STIM donor.
Our study demonstrates impairment of the parasympathetic nervous system during BD and inhibition of serum TNFα through vagal stimulation. Vagus nerve stimulation variably affected gene expression in donor organs and improved renal function in recipients.

overall_design: Gene expression in brain dead (BD) induced rat (with and without vagal stimulation) was compared with that of Non brain-dead ventilated control (NBD)

first: Simone

last: Hoeger

first: Claudia

last: Bergstraesser

first: Jochen

last: Selhorst

first: Johann

last: Fontana

first: Rainer

last: Birck

first: Ruediger

last: Waldherr

first: Gritje

last: Beck

first: Carsten

last: Sticht

first: Marc

last: Seelen

first: Willem

last: van Son

first: Henri

last: Leuvenink

first: Rutger

last: Ploeg

first: Peter

last: Schnuelle


title: Gene expression profiling of grape-bud response to two alternative dormancy-release stimuli.

city: Bet-Dagan

first: Ron

last: Ophir

address: POB 6

department: Fruit Tree Sciences

institute: Agricultire Research Organization

summary: A grape-bud-oriented genomic platform was produced for a large-scale comparative analysis of bud responses to two stimuli of grape-bud dormancy release, hydrogen cyanamide (HC) and heat shock (HS). The results suggested considerable similarity in bud response to the stimuli, both in the repertoire of responding genes and in the temporary nature of the transcriptome reprogramming. Nevertheless, the bud response to HC was slower, more condensed and stronger, as reflected by a higher number of regulated genes and a higher intensity of regulation compared to the response to HS.

platform_organism:
Vitis vinifera
Vitis riparia

overall_design:
To facilitate large-scale comparative analysis of early changes in the bud transcriptome by cDNA microarray, HC and HS were applied to canes collected from three vineyards, located in different regions, in three different years. This experimental scheme resulted in two true biological replicates for each treatment, differing in both timing and location, and loop design of technical replicates within time series.
Consistent with our previous studies, both application of 5% Dormex (HC) and incubation for 1 h in 50oC water (HS) resulted in increased bud-break rates compared to respective controls. Bud break of HS-treated and HC-treated buds started 10 to 12 days after treatment. Three weeks after treatment, HS-treated buds exhibited 100% bud break while HC-treated buds had reached 80% bud break. The control showed significantly lower levels of bud break during this period. Bud material was collected from control, HC- and HS-treated cuttings at six time points (3, 6, 12, 24, 48 and 96 h) after the treatments and used to prepare total RNA samples.

first: Etti

last: Or


title: Iron (Fe) deficiency in Citrus

city: Valencia

first: Miguel

last: Perez-Amador

state: Valencia

address: Avda. de los Naranjos s/n

institute: Inst. Biologia Molecular y Celular de Plantas (IBMCP-CSIC)

summary:
Transcription profiling of citrus rootstock Poncirus trifoliata (L.) Raf.

Keywords: Abiotic stress (Iron chlorosis)

overall_design: Total RNA from four replicates for each sample category (Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA or without Fe-EDDHA) were generated and compared.

first: M

last: Forner-Giner

first: J

last: Llosa

first: Gemma

last: Ancillo


title: P16INK4a mediated supperssion of telomerase in normal and malignant human breast cells

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: The cyclin-dependent kinase inhibitor p16INK4a (CDKN2A) is an important tumor-suppressor gene frequently inactivated in human tumors.  p16 suppresses the development of cancer by triggering an irreversible arrest of cell proliferation termed cellular senescence.  Here, we describe another anti-oncogenic function of p16 in addition to its ability to halt cell cycle progression.  We show that transient expression of p16 stably represses the hTERT gene, encoding the catalytic subunit of telomerase, in both normal and malignant breast epithelial cells.  Short-term p16 expression increases the amount of histone H3 trimethylated on lysine 27 (H3K27) bound to the hTERT promoter, resulting in transcriptional silencing, likely mediated by polycomb complexes.  Our results indicate that transient p16 exposure may prevent malignant progression in dividing cells by irreversible repression of genes, such as hTERT, whose activity is necessary for extensive self-renewal.

overall_design: 27 samples were analyzed to study three histone modifications (H3K4me3, H3K9me3, H3K27me3) in three different cell lines.  Each combination of histone modification and cell line had three biological replicates (A,B,C).

first: Alexey

middle: V

last: Bazarov

first: Curtis

last: Hines

first: Leonard

last: Lee

first: Ekaterina

last: Bassett

first: Alain

last: Beliveau

first: Eric

last: Campeau

first: Rituparna

last: Mukhopadhyay

first: WonJae

first: Sonya

last: Melodyev

first: Yuri

last: Zaslavsky

first: Francis

last: Rodier

first: Jean

last: Benhattar

first: Judith

last: Campisi

first: Paul

last: Yaswen


title: Identification of Sfh and H-NS binding sites in the Salmonella Typhimurium genome

first: Shane

last: Dillon

summary:
The global regulator H-NS represses transcription in gram negative bacteria. Sfh is a homologue of H-NS and is encoded by plasmid pSfR27. Sfh provides a 'stealth' function that allows pSfR27 to be transmitted to a new host without disrupting the competitive fitness of the new host
We used ChIP-on-chip to profile Sfh (3xFLAG-tagged) and H-NS binding sites in Salmonella Typhimurium strain SL1344 and found that Sfh provides its 'stealth' function by targeting a sub-set of H-NS bound genes that display reduced levels of H-NS occupancy with the SL1344 chromosome upon acquisition of plasmid pSfR27

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Identification of Sfh binding sites in strains SL1344 (pSfR27) and SL1344 hns (pSfR27) as well as identification of H-NS binding sites in strains SL1344, SL1344 (pSfR27), and SL1344 (pSfR27) sfh

first: Andrew

last: Cameron

first: Karsten

last: Hokamp

first: Sacha

last: Lucchini

first: Jay

last: Hinton

first: Charles

middle: J

last: Dorman


title: Sex biased gene expression in 17 weeks old chicken (ovary, testes)

city: Praha

first: Libor

last: Morkovsky

address: Vinicna 7

department: Department of zoology

country: Czech Republic

institute: Charles University in Prague

summary: Sex chromosomes are characterized by a non-random content of genes with preferential expression in one sex. The mechanisms which are responsible for this phenomenon are, however, largely unresolved. To elucidate selective forces shaping the Z chromosome gene content in chicken, we analyzed microarray data from adult and embryonic gonads (the latter already available in GEO Series GSE8693).

overall_design:
Total RNA from gonads of 8 males and 8 females was used for hybridization to Affymetrix GeneChip® Chicken Genome Arrays. Prior to hybridization the samples were combined in equal quantities into 4 pools (4 testes/ovary samples in each pool), 2 of them representing testis and 2 ovary.
All four GeneChips met Affymetrix quality control criteria. Furthermore, all chips were checked by methods based on probe level robust linear model fitting provided by "affyPLM" package (Bolstad, 2007). None of the chips showed any signs of abnormality.

first: Radka

last: Storchova

first: Jiri

last: Plachy

first: Robert

last: Ivanek

first: Petr

last: Divina

last: Hejnar


title: p55 and p75 tumor necrosis factor receptor double KO and systemic lupus erythematosis

city: Los Angeles

first: Chaim

middle: O

last: Jacob

address: 2011 Zonal Ave

department: Medicine/GI division

institute: University of Southern California

summary:
Gene expresion comperison of p55/p75 double knock and it control B57B6 identified a number of inflammatory genes and cytokines genes play important roles in this study.

TNFa has both pro-inflammatory and immunoregulatory functions. Whereas a protective role for TNF administration in SLE-prone (NZB x NZW)F1 mice has been established, it remains uncertain whether this effect segregates at the individual TNF receptors (TNFR). We generated SLE-prone New Zealand Mixed 2328 mice genetically deficient in TNF receptor 1, in TNF receptor 2, or in both receptors. Doubly-deficient mice developed accelerated pathological and clinical nephritis with elevated levels of circulating IgG anti-dsDNA autoantibodies and increased numbers of CD4+ T lymphocytes, especially activated memory (CD44highCD62Llow) CD4+ T cells. We show that these cells expressed a Th17 gene profile, were positive for IL-17 intracellular staining by FACS, and produced exogenous IL-17 in culture. In contrast, immunological, pathological, and clinical profiles of mice deficient in either TNF receptor alone did not differ from those in each other or from those in wild-type controls. Thus, total ablation of TNFa-mediated signaling was highly deleterious to the host in the NZM 2328 SLE model. These observations may have profound ramifications for the use of TNF- and TNF receptor-antagonists in human SLE and related autoimmune disorders, as well as demonstrate, for the first time, the association of the Th17 pathway with an animal model of SLE.

overall_design: CD4+CD44highCD62Llow/neg  spleen cells were isolated from 5-month-old female p55/p75 double knockout (DKO) NZM 2328 mice or C57BL/6 mice by depleting CD19+ B cells with magnetic beads (Dynal Biotech) followed by flow cytometry sorting .  Total RNA was extracted from each sorted cell preparation using RNA STAT-60 isolation reagents (Tel-Test Inc. Friendswood, TX). First strand cDNAs were prepared from 250-500 ng total RNA of each sample using First Strand cDNA Kit (Fermentas Inc. Hanover, MD). Template cDNAs were characterized in technical quadruplicates using two different RT2 Profiler PCR Arrays: the mouse Th1-Th2-Th3 array and the Th-17 pathway PCR Array for Autoimmunity & Inflammation (SuperArray Bioscience, Fredrick, MD).

first: C

first: W

last: Stohl


title: Molecular response of the coral Acropora millepora to three settlement and/or metamorphosis induced stimuli

city: Canberra

first: Lauretta

last: Grasso

state: ACT

address: Biology Place

department: Research School of Biological Sciences

country: Australia

institute: Australian National University

summary: Two known settlement/metamorphosis inducing stimuli (crustose coralline algae, and ethanolic extract of crustose coralline algae) and one stimulus which just induces metamorphosis (LWamide) were used to stimulate competent planula larvae of the coral Acropora millepora.  Samples were taken 0.5h, 4h and 12h post induction isolate the genes controlling settlement and metamorphosis in this coral.

overall_design: All samples were labeled with Cy3 and co-hybridised with a Cy5 labeled common reference sample.  There were two replicates. The Cy5 labeled common reference was a pool of equal parts of all of the test samples. For hybridisation, the same quantity of RNA as used for the test sample was Cy5 labeled for co-hybridisation with the Cy3 labeled sample.

last: Negri

first: David

last: Hayward

last: Miller

first: Eldon

middle: E

last: Ball


title: Differential Expression genes between Moniezia expansa and Moniezia benedini

city: Shi Hezi

first: Wenjuan

last: Zhao

state: Xinjiang

address: Wu Yi Road 221#

institute: The Breed & Biotechnology Key Laboratory of Sheep in XinJiang Bingtuan

summary: We used complementary DNA microarray to analyze the gene expression profiles different between Moniezia expansa and Moniezia benedini. A total of 4056 sequences including full length and partial complementary DNAs representing novel, known, and control genes were analyzed. We utilized cDNA array for detection of gene expression profiles of different proglottids of M.expansa and M.benedini. The present study provides some interesting data that only expressed in M.expansa

sample_organism:
Moniezia expansa
Moniezia benedeni

overall_design: mature proglottids, immature proglottids, gravid proglottids of M.benedini vs common reference scolex-neck proglottids tissue of M.expansa. 2 biological replicates for each experiments.

first: Hui

last: Zhang

first: Xinwen

last: Bo

first: Xinhua

last: Wang

first: Lichao

last: Kang

first: Tingde

last: Lv

first: Jianjuan

last: Zhu


title: Small RNA survey of mouse genome

city: Brisbane

first: Larry

last: Croft

state: QLD

address: The University of Queensland, St Lucia

institute: Institute for Molecular Bioscience

summary:
Using criteria based on known examples, we identified approximately 1.7 million and 2.4 million sequences encoding putative miRNA precursor (stem-loop) structures in the mouse and human genomes, respectively, as well as large numbers of such structures in the genomes of fish, fruitfly and nematode worm. These predictions were then tested using high density custom microarrays containing modified oligonucleotides interrogated with purified small RNAs from different tissues. We found that 19% of 4,006 randomly chosen mouse predictions and 40% of 1,859 randomly chosen human predictions gave positive signals with small RNA isolated from whole 10-12 day embryos and a mixture of brain and testis, respectively, 84% of which hybridized to only one strand of the predicted stem-loop structure, whereas only 2% and 12% of equivalent random mouse and human predictions were positive. There was no difference in the validation rates between sequences exhibiting conservation and those that did not. High validation rates were also observed with predictions from fish, fly and worm genomes. Northern blot analysis of the array-positive mouse predictions confirmed that the vast majority of these sequences were detectable as small RNAs whose sizes ranged from 20-110 nucleotides. Taking into account false negative rates of the prediction and detection of known miRNAs, and assuming that this holds for other small RNAs, we estimate that there are 1 million small RNAs expressed in mouse and 3 million small RNAs in human.
Keywords: genomic survey of small RNAs

overall_design: Stemloops were identified in the mouse and human genome using RNALfold with a window size of 110nt. Folding energy and other criteria were used to filter the structures into a set of miRNA-like stems. Stems were chosen randomly and probes designed against the stem regions. Stems were called present if one of the stem probes was more than 4 standard deviations above the signal distribution of mRNA degradation contamination probes designed against GAPDH and beta-actin.

first: Ryan

last: Taft

first: Marjan

last: Askarian Amiri

first: Xiaochuan

last: Zhou

first: Cas

last: Simons

first: John

last: Mattick


title: Prognostic analysis of mantle cell lymphoma genomes

city: Vancouver

first: Ronald

last: deLeeuw

state: British Columbia

department: Cancer Genetics

country: Canada

institute: BC Cancer Research Centre

summary: Mantle cell lymphoma is characterized by a t(11;14) chromosomal translocation; however, it alone is insufficient to result in the disease.  A number of secondary genetic alterations have been proposed as essential in MCL pathogenesis.  Amongst these, numerous copy number altered regions remain ill-defined, both for location and prognostic significance.  In this study we examined in detail the genomes of a panel of 52 MCL cases.  Relating gene dosage alterations to disease outcome, we found seven loci that correlated with overall survival.  A survival model was constructed based on four of these loci (P = 5.87 x 10-6).  Using serial analysis of gene expression and quantitative PCR we investigated the expression of genes within these altered regions and determined that CCNI and CCNG2 may be important in MCL pathogenesis (P = 0.0201 and P = 0.0292, respectively).  Our findings reinforce the hypothesis that cell cycle deregulation and apoptosis are key factors in MCL pathogenesis.

overall_design: Array CGH, Long-SAGE, and qPCR were utilized to determine regions of the genome that have prognostic significance when altered in copy number in MCL.

first: Chad

last: Malloff

first: Nathalie

last: Johnson

first: Yulei

last: Shen

first: Martin

last: Dyer

first: Joseph

last: Connors

first: Randy

last: Gascoyne

first: Wing

last: Chan

first: Douglas

last: Horsman

first: Wan

middle: L

last: Lam


title: Genome-wide transcriptional profiling of NF1-haploinsufficiency in human: ECACC kindred

status: Public on Nov 30 2009

city: Bethesda

first: Alexander

last: Pemov

address: 49 Convent Drive

institute: National Institutes of Health

summary: Neurofibromatosis type 1 (NF1) is a common monogenic tumor-predisposition disorder that arises secondary to mutations in the tumor suppressor gene NF1. Haploinsufficiency of NF1 fosters a permissive tumorigenic environment through changes in signalling between cells; however, the intracellular mechanisms for this tumor-promoting effect are less clear. We hypothesized that the genetic effects of NF1-haploinsufficiency may be discerned by comparison of genome-wide transcriptional profiling in somatic, non-tumor cells (LCLs) from NF1-affected and –unaffected individuals.

overall_design:
Total RNA obtained from lymphoblastoid cell lines (LCLs) from NF1-affected individuals was compared to total RNA from LCLs of NF1-unaffected controls.

The supplementary file 'GSE18445_non-normalized_data.txt' contains non-normalized data for Samples GSM459556-GSM459561.

middle: R

last: Stewart


title: Genome-wide transcriptional profiling of Nf1-haploinsufficiency in mouse

summary: Neurofibromatosis type 1 (NF1) is a common monogenic tumor-predisposition disorder that arises secondary to mutations in the tumor suppressor gene NF1. Haploinsufficiency of NF1 fosters a permissive tumorigenic environment through changes in signalling between cells; however, the intracellular mechanisms for this tumor-promoting effect are less clear. We hypothesized that the genetic effects of NF1-haploinsufficiency may be discerned by comparison of genome-wide transcriptional profiling in somatic, non-tumor cells from NF1-affected and –unaffected individuals. As a cross-species filter for heterogeneity, we compared the results from two human kindreds to whole-genome transcriptional profiling in spleen-derived B-cells from age- and gender-matched Nf1+/- and wild-type mice.

overall_design:
Total RNAs obtained from spleen-derived B-cells from age- and gender-matched Nf1+/- and wild-type mice were used for whole-genome transcriptional profiling as a cross-species filter for changes specific to NF1-haploinsufficiency.

The supplementary file 'GSE18447_non-normalized_data.txt' contains non-normalized data for Samples GSM459562-GSM459573.


title: Arabidopsis unfertilized pistil development and senescence

first: Pablo

last: Carbonell

address: Ingeniero Fausto Elio

institute: IBMCP-CSIC

summary:
Transcription profiling of post-anthesis unfertilized pistil development and senescence in Arabidopsis, in a serie including samples from seven different stages according to pistil age in days post-anthesis (dpa). The time course started at anthesis and ended at 12-14 dpa, several days later of the loss of fruit set capacity.

Keywords: Developmental time course

overall_design: Unfertilized pistils were obtained growing under low humidity cer6-2 conditional male sterile mutant of Arabidopsis in Ler background. The seven stages considered were: 0-1 dpa, 2-3 dpa, 4-5 dpa, 6-7 dpa, 8-9 dpa 10-11 dpa and 12-14 dpa. Two biological replicas with two technical replicas each were performed for each stage. The biological replicas were grown independently, and all the samples of each one were harvested simultaneously. Amplified RNA from each sample was hibridized together with a global reference over the DNA microarray. The reference was generated from an equimolar mix of amplified RNAs from each of the seven samples of the corresponding biological replica. Amplified RNA from each sample was labelled separately with Cy5 and with Cy3, and each labelling was compared in the DNA microarray with Cy3-labelled and with Cy5-labelled RNA from the reference mix, respectively.

first: Miguel

last: Perez-Amador