title: SitkaSpruce_FB3-425_Bark_UntreatedControl_SelfHybridization

first: Joerg

last: Bohlmann

summary:
As part of a larger conifer genomics project, we developed a new 21.8K cDNA microarray containing 21,843 spotted ESTs from spruce (Picea spp.).  To evaluate the performance of the array we conducted four technical replicate self-self hybridizations using untreated control bark RNA pooled from four biological replicates.  The objectives were to determine: 1) the linear dynamic range of expression detection of the array; 2) the level of non-specific hybridization to negative control elements on the array; and 3) the overall technical reproducibility of the array.
Keywords: Array performance evaluation using self-self hybridizations.

overall_design: To assess performance of the spruce 21.8K microarray, a model containing a dye effect and a treatment effect for untreated control (C) minus C' was fit using data from four microarray slides. The C minus C' effect was computed by assigning two of the self-hybridized arrays to be Cy5-Cy3 and two to be Cy3-Cy5. Three analyses were done such that each self-hybridized array was paired with each other self-hybridized array only once, either as a Cy5-Cy3 or a Cy3-Cy5 combination.  Expression variance was derived from technical variance between slides. The ratio of the C minus C' parameter estimate to the standard error was used to calculate a t statistic, from which a P value was obtained. The Q value for each effect and gene was calculated for each of the two models to adjust for the false discovery rate [Storey & Tibshirani (2003) Proc. Natl. Acad. Sci. USA. 100: 9440-9445].  All statistical analyses were performed within the R statistical package (www.r-project.org/).

first: Steven

last: Ralph


title: Comparative Genomic Hybridization of Leishmania major methotrexate resistant strains vs wild-type LV39

status: Public on May 31 2008

city: Québec

first: Marc

last: Ouellette

state: Québec

address: 2705 bd Laurier

department: Département médecine

country: Canada

institute: Université Laval

summary:
CGH analysis of the drug resistant strain L. major MTX60.4 vs the wild-type strain LV39
The full-genome DNA microarrays includes one 70-oligonucleotides probe for each gene of L.major LV39

Keywords: drug resistance

platform_organism:
Leishmania major
Leishmania infantum

overall_design: Two-condition experiment, resistant strain MTX60.4 vs wild-type LV39. Three biological replicates for each strain, independently grown and harvested. One replicate per array

first: J

middle: M

last: Ubeda

first: D

last: Légaré

first: F

last: Raymond

first: A

middle: A

last: Ouameur

first: S

last: Boisvert

first: P

last: Rigault

last: Corbeil

first: M

last: Tremblay

last: Olivier

first: B

last: Papadopoulou


title: Retroviral insertional mutagenesis screen in a C/EBPalpha proliferative genetic background

status: Public on Jun 01 2008

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary:
The CCAAT enhancer binding protein alpha (C/EBPalpha) transcription factor plays a key role in the regulation of growth and differentiation of the granulocytic lineage in the hematopoietic system and CEBPA (encoding C/EBPalpha) is often mutated or deregulated in AML patients. Consistently, mice lacking C/EBPalpha have no mature neutrophils and die within a few hours. However, homozygous knockin mice in which wild type Cebpa has been replaced with a mutant allele (BRM2), which abolish the growth-repressing ability of C/EBPalpha, are viable, but at 8 weeks of age they display myeloid dysplasia with absence of neutrophil granulocytes. Strikingly, in older CebpaBRM2/BRM2 knockin mice the myeloid dysplastic phenotype progress into other myeloid malignancies such as myeloid proliferative syndrome and acute myeloid leukemia-like malignancy. This strongly suggests that secondary mutations in other loci must occur when developing leukemia in the CebpaBRM2/BRM2.
In order to identify genes that cooperate with Cebpa mutations in the development of leukemia in CebpaBRM2/BRM2 mice a so-called retroviral insertion mutagenesis screen was performed. Inbred newborn CebpaBRM2/BRM2 and wildtype mice were injected with SRS19-6 retrovirus, which incorporated into the genome and resulted in activation of oncogenes and leukemic progression. When leukemia was evident the mice were euthanized and analyzed. As expected the CebpaBRM2/BRM2 mice had a shorter latency than wildtype mice (186 vs. 276 days). The mice had enlarged spleen, thymus, and/or lymph nodes and were thoroughly investigated by histology, flow cytometry and southern in order to determine the leukemic phenotypes. Most of the CebpaBRM2/BRM2 mice developed an AML-like phenotype, whereas T cell leukemias were most prominent in wildtype mice, showing that mutating Cebpa specifically directs leukemic progression towards a myeloid direction. Genomic instability was analyzed by CGH. Finally, the retroviral insertion loci were identified through a splinkerette-aided PCR strategy. This led to the identification of several novel putative and previously unexplored oncogenes, which might collaborate with mutated Cebpa in the development of AML.
Keywords: Disease state analysis

overall_design: In order to identify genes that cooperate with Cebpa mutations in the development of leukemia in CebpaBRM2/BRM2 mice a so-called retroviral insertion mutagenesis screen was performed. Inbred newborn CebpaBRM2/BRM2 and wildtype mice were injected with SRS19-6 retrovirus, which incorporated into the genome and resulted in activation of oncogenes and leukemic progression. When leukemia was evident the mice were euthanized and analyzed. GDNA from tumour tissues were analyzed by CGH using tail gDNA as reference.


title: Percutaneous Collagen Induction (PCI) in rat

city: Hanover

first: Cornelia

last: Repenning

address: Callinstrasse 3

department: Institut fuer Technische Chemie

country: Germany

institute: Leibniz University of Hanover

summary: The purpose of the present study is to determine the effect of Percutaneous Collagen Induction (PCI) on the epidermis and dermis, including the systemic inflammatory response on gene expression level using microarray analysis. PCI Therapy is an alternative for safely treating wrinkles and scars and smoothening the skin. Therefore animal experiments were performed using 31 male Sprague-Dawley rats (350–375 g), age 4 month, randomly assigned into three groups: group (A) (n=24: needling plus skin care), group (B) (n=6: skincare only, controls after 24 h) and group (C) (n=1: negative control). Rats were anesthetized, shaved, and received a 30% total body surface area (TBSA) scald needling (10min) to induce percutaneous collagen, using a medical needling instrument (Environ® Medical Roll-CITTM, Vivida SA cc, Cape Town, South Africa). After needling surgery, the rats were immediately prepared with high levels of vitamin A cream and vitamin C cream, applied topically after cleaning once per day. The control group (C) rats received no injury, no skin care, no treatment, no anesthesia, and no analgesia. Gene expression analyses were performed 1 h, 24 h, 2, 4, and 8 weeks after PCI surgery. To confirm RNA expression in rat skin, self developed microarrays including genes like cytokines, such as vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF 2), keratinocyte growth factor (KGF), epidermal growth factor (EGF), and transforming growth factors (TGF ß1, ß2, ß3) were used.

overall_design: Results from 6 microarrays are summarized in this study. The samples originate from different time points after needling surgery mentioned above. Microarrays were hybridized in a loop design with one common reference using a dye swap approach.

first: Matthias

middle: C

last: Aust

first: Frank

last: Stahl

first: Thomas

last: Scheper

first: Kerstin

last: Reimers

first: Peter

last: Vogt


title: Gene expression profiles of wild type and Mecp2-null mice in three different regions of the brain

city: Madrid

first: Rocio

middle: G.

last: Urdinguio

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Pathology Program

country: Spain

institute: Spanish National Cancer Centre (CNIO)

summary: Background. Rett syndrome (RTT) is a complex neurodevelopmental disorder that is one of the most frequent causes of mental retardation in women. A great landmark in research in this field was the discovery of a relationship between the disease and the presence of mutations in the gene that codes for the methyl-CpG binding protein 2 (MeCP2). Currently, MeCP2 is thought to act as a transcriptional repressor that couples DNA methylation and transcriptional silencing. The present study aimed to identify new target genes directly regulated by Mecp2 in a mouse model of RTT. Methodology. We have compared the gene expression profiles of wild type (WT) and Mecp2-null (KO) mice in three regions of the brain (cortex, midbrain, and cerebellum) by using cDNA microarrays. The results obtained were confirmed by quantitative real-time PCR. Subsequent chromatin immunoprecipitation assays revealed seven direct target genes of Mecp2 bound in vivo (Dlk1, Mobp, Plagl1, Ddc, Mllt2h, Eya2, and S100a9), and two overexpressed genes due to an indirect effect of a lack of Mecp2 (Irak1 and Prodh). Bisulfite sequencing analysis of the methylation patterns of promoters of the described genes showed no differences between WT and KO mice, demonstrating that methylation differences were not the cause of the observed expression changes. Moreover, the regions bound by Mecp2 were always methylated, suggesting the involvement of the methyl-CpG binding domain of the protein in the mechanism of interaction. Conclusions. We identified new genes that are overexpressed in KO mice and are excellent candidate genes for involvement in various features of the neurodevelopmental disease. Our results demonstrate new targets of MeCP2 and provide us with a better understanding of the underlying mechanisms of RTT.

overall_design: Comparative experiment: Mecp2-null (KO) mice vs. their corresponding age-mated wild type (WT) littermates (CONTROLS). Four couples of KO-WT animals are used and three different brain regions are studied from each couple; cortex, midbrain, and cerebellum.

middle: G

first: Manel

last: Esteller


title: Discovery of the targets of the immune response to chronic lymphocytic leukemia in 2 patients using protein microarrays

city: Cleveland

first: Ovidiu

last: Marina

state: OH

address: 10900 Euclid Ave

department: School of Medicine

country: USA

institute: Case Western Reserve University

summary:
The binding of serum immunoglobulins to proteins was compared using serum from after and before an immunotherapeutic intervention (donor lymphocyte infusion) in two patients who had relapsed chronic lymphocytic leukemia (CLL) after bone marrow transplant. One Invitrogen ProtoArray was used for each sample. Significant interactions were determined by comparing the before and after samples for each patient separately, using the Concentration-Dependent Analysis described in Marina et al., J Proteome Res, 2008.
One sample from before and one sample from after immunotherapy were tested for each patient.
Keywords: Immune response discovery


title: Genome-wide analysis of esopageal adenocarcinoma tumor biopsy using high-density single-nucleotide polymorphism arrays.

city: Herston

first: Derek

middle: John

last: Nancarrow

state: Queensland

address: 300 Herston Road

department: Genetics & Population Health

country: Australia

institute: Queensland Institute of Medical Research

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

summary:
We applied whole-genome single nucleotide polymorphism (SNP) arrays to define a comprehensive genetic profile of 23 esophageal adenocarcinoma (EAC) primary tumor biopsies based on loss of heterozygosity (LOH) and DNA copy number changes. Alterations were common, averaging 97 (range 23-208) per tumor. LOH and gains averaged 33 (range 3-83) and 31 (range 11-73) per tumor, respectively. Copy neutral LOH events averaged 27 (range 7-57) per EAC. We noted 126 homozygous deletions (HDs) across the EAC panel (range 0-11 in individual tumors). Frequent HDs within FHIT (17/23), WWOX (8/23) and DMD (6/23) suggest a role for common fragile sites or genomic instability in EAC etiology. HDs were also noted for known tumor suppressor genes (TSGs) including: CDKN2A, CDKN2B, SMAD4 and GALR1, and identified PDE4D and MGC48628 as potentially novel TSGs. All tumors showed LOH for most of chromosome 17p, suggesting that TSGs other than TP53 maybe targeted. Frequent gains were noted around MYC (13/23), BCL9 (12/23), CTAGE1 (14/23) and ZNF217 (12/23). Thus, we have confirmed previous reports indicating frequent changes to FHIT, CDKN2A, TP53 and MYC in EAC and identified additional genes of interest. Meta analysis of previous genome-wide EAC studies together with the data presented here, highlighted consistent regions of gain on 8q, 18q and 20q, and multiple LOH regions on 4q, 5q, 17p and 18q, suggesting that more than one gene may be targeted on each of these chromosome arms. The focal gains and deletions documented here are a step towards identifying the key genes involved in EAC development.
Keywords: High Density SNP array

overall_design: Here we use Illumina 317K whole-genome single-nucleotide polymorphism arrays to define a comprehensive allelotype of melanoma based on loss of heterozygosity (LOH) and copy number changes in a panel of 23 esophageal adenocarcinoma (EAC) primary tumor biopsies. Each EAC was paired to normal squamous biopsy from 40328 (GSM266078) to generate the log_R_ratio.

middle: J

first: Herlina

middle: Y

last: Handoko

first: Mark

last: Smithers

first: David

last: Gotley

first: Paul

last: Drew

middle: I

last: Watson

first: Andrew

middle: D

last: Clouston

first: Nicholas

middle: K

last: Hayward

last: Whiteman


title: Mfaveolata time course bleaching experiment

city: San Francisco

first: Michael

last: DeSalvo

state: CA

department: Department of Anesthesia

institute: UC San Francisco

summary:
The declining health of coral reefs worldwide is likely to intensify in response to continued anthropogenic disturbance from coastal development, pollution, and climate change.  In response to these stresses, reef-building corals may exhibit bleaching, which marks the breakdown in symbiosis between coral and zooxanthellae.  Mass coral bleaching due to elevated water temperature can devastate coral reefs on a large geographic scale.  In order to understand the molecular and cellular basis of bleaching in corals, we have measured gene expression changes associated with thermal stress and bleaching using a cDNA microarray containing 1,310 genes of the Caribbean coral Montastraea faveolata.  In a first experiment, we identified differentially expressed genes by comparing experimentally bleached M. faveolata fragments to control non-heat-stressed fragments.  We also identified differentially expressed genes during a time course experiment with four time points across nine days.  Results suggest that thermal stress and bleaching in M. faveolata affect the following processes: oxidative stress, Ca2+ homeostasis, cytoskeletal organization, cell death, calcification, metabolism, protein synthesis, heat shock protein activity, and transposon activity. These results represent the first large-scale transcriptomic study focused on revealing the cellular foundation of thermal stress-induced coral bleaching.  We postulate that oxidative stress in thermal-stressed corals causes a disruption of Ca2+ homeostasis, which in turn leads to cytoskeletal and cell adhesion changes, decreased calcification, and the initiation of cell death via apoptosis and necrosis.
Keywords: thermal stress response, time course, coral bleaching

overall_design: Time course with 4 time points and 4 biological replicates per time point.  Each biological replicate at each time point was hybridized to a pooled reference control sample containing RNA from all control non-heat-stressed coral fragments.

first: Christian

middle: R

last: Voolstra

first: Shinichi

last: Sunagawa

first: Jodi

last: Schwarz

first: Jonathon

middle: H

last: Stillman

first: Mary

last: Co

first: Alina

last: Szmant

first: Monica

last: Medina


title: Batch wt vs hyper +_- pABA Normal int_Filtered fg-bg2

city: Ede

first: Arno

last: Wegkamp

address: Kernhemseweg 2

institute: NIZO food research

summary:
Transcriptional analysis upon the overexpression of the folate gene cluster on a high copy plasmid when compared to an empty vector in the lactic acid bacterium L. plantarum. The transcriptional response was determined for both strains in the presence and absence of pABA thereby using the hybridisation sceme as described in the data processing section.
Keywords: response to folate gene cluster overexpression and pABA treatment

overall_design: The batch experiment with and without pABA scheme consisted of a loop design with 21 microarrays with the following samples hybridized on one array and labeled with Cy3 and Cy5, respectively: C1+P and F1+P, F1+P and C2+P, C2+P and F3+P, F3+P and C3+P, C3+P and F2+P, F2+P and C1+P, C1+P and C2+P, F2+P and F3+P, C1-P and F1-P, F1-P and C2-P, C2-P and F3-P, F3-P and C3-P, C3-P and F2-P, F2-P and C1-P, C1-P and C2-P, F2-P and F3-P, C3-P and F1+P, F2+P and C1-P, C2+P and F3-P, F1-P and C3+P, and F2+P and F1-P. Here, C1+P, C2+P, C3+P, F1+P, F2+P, and F3+P represent biological triplicates of the L. plantarum harboring pNZ7021 and pNZ7026, respectively, when grown in batch in the presence of pABA. The C1-P, C2-P, C3-P, F1-P, F2-P, and F3-P, represents the L. plantarum harboring pNZ7021 and pNZ7026, respectively, when grown in batch in the absence of pABA.

first: Astrid

last: Mars

first: Magda

last: Faijes

first: Douwe

last: Molenaar

first: Ric

last: de Vos

first: Sebastian

last: Klaus

last: Hanson

first: Willem

first: Eddy

last: Smid


title: Mfaveolata single-time point bleaching experiment

summary:
The declining health of coral reefs worldwide is likely to intensify in response to continued anthropogenic disturbance from coastal development, pollution, and climate change.  In response to these stresses, reef-building corals may exhibit bleaching, which marks the breakdown in symbiosis between coral and zooxanthellae.  Mass coral bleaching due to elevated water temperature can devastate coral reefs on a large geographic scale.  In order to understand the molecular and cellular basis of bleaching in corals, we have measured gene expression changes associated with thermal stress and bleaching using a cDNA microarray containing 1,310 genes of the Caribbean coral Montastraea faveolata.  In a first experiment, we identified differentially expressed genes by comparing experimentally bleached M. faveolata fragments to control non-heat-stressed fragments.  We also identified differentially expressed genes during a time course experiment with four time points across nine days.  Results suggest that thermal stress and bleaching in M. faveolata affect the following processes: oxidative stress, Ca2+ homeostasis, cytoskeletal organization, cell death, calcification, metabolism, protein synthesis, heat shock protein activity, and transposon activity. These results represent the first large-scale transcriptomic study focused on revealing the cellular foundation of thermal stress-induced coral bleaching.  We postulate that oxidative stress in thermal-stressed corals causes a disruption of Ca2+ homeostasis, which in turn leads to cytoskeletal and cell adhesion changes, decreased calcification, and the initiation of cell death via apoptosis and necrosis.
Keywords: thermal stress response; coral bleaching

overall_design: 5 control and 5 heat-stressed RNA samples were hybridized in a 5-replicate dye-swap design (10 total hyb's).

last: Coffroth


title: Global monitoring of autumn gene expression within and among populations of Sitka spruce

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

institute: University of British Columbia

summary:
Cold acclimation in conifers is a complex process, the timing and extent of which reflects local adaptation and varies widely along latitudinal gradients for many temperate and boreal tree species. In spite of their ecological and economic importance, little is known about the global changes in gene expression that accompany autumn cold acclimation in conifers. Using three populations of Sitka spruce (Picea sitchensis) spanning the species range, and a Picea cDNA microarray with 21,840 unique elements, we monitored within and among-population gene expression during the fall. Microarray data were validated for selected genes using real-time PCR. Similar numbers of genes were significantly two-fold upregulated (1,257) and downregulated (967) between late summer and early winter. Among those upregulated were dehydrins, pathogenesis-related/antifreeze genes, carbohydrate and lipid metabolism genes, and genes involved in signal transduction and transcriptional regulation. Among-population microarray hybridizations at early and late autumn time points revealed substantial variation in the autumn transcriptome, some of which may reflect local adaptation. Our results demonstrate the complexity of cold acclimation in conifers, highlight similarities and differences to cold tolerance in annual plants, and provide a solid foundation for functional and genetic studies of this important adaptive process in conifers.
Keywords: Time course

overall_design:
Foliage for RNA extraction was obtained from four-year-old Sitka spruce seedlings, which were grown from seed collected across the species range in a raised-bed outdoor common garden in Vancouver, BC, Canada (49º N) (Mimura and Aitken, 2007, Heredity). Needle tissues from current year upper lateral shoots, separated from stem and bark tissue, were collected at five time points between late summer and early winter, 2004. Three populations were chosen for sampling: Valdez, Alaska, USA (61º N) (AK), Prince Rupert, British Columbia, Canada (54º N) (BC) and Redwood, California, USA (41º N) (CA) (Figure 1a). Needle samples (~1g) were taken from eight individuals in the BC population on each of the five dates (Aug. 30, Oct. 18, Nov. 24, Dec. 1, and Dec. 13). Eight individuals from the AK and CA populations were also sampled on the second and fourth dates, as well as eight additional individuals from the BC population. Tissues were flash frozen in an N2 vapor tank immediately upon collection, and subsequently stored at -80°C until processing.
To decrease the effects of biological variance among individual seedlings within populations, equal amounts of foliar tissue were pooled from four individuals prior to RNA extraction. Two pools were collected at each time point for each population, and total RNA was extracted following a previously published protocol (Kolosova et al., 2004).
Slides were scanned and spot intensity quantified using ImaGene software (BioDiscovery, Inc., El Segundo, CA). To correct for background intensity, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities. Data were then normalized by variance stabilizing normalization (VSN) to compensate for nonlinearity of intensity distributions (Huber et al., 2002).
To identify significant changes in gene expression, a linear mixed-effects model was fit to the normalized intensities in the Cy3 and Cy5 channels of the 32 microarray slides. The model contained an adjustment for dye bias, an array effect indicating which Cy5/Cy3 pair was on each array, a treatment effect indicating sample population and time point, and a random effect to adjust for repeated measures on the same biological sample (Kerr et al., 2000). P-values were computed for each gene-by-treatment effect and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003).

first: Jason

last: Holliday

first: Steven

last: Ralph

first: Richard

last: White

first: Sally

middle: N

last: Aitken


title: Thiosulfate vs Sulfate as electron acceptor in Sulfate reduction

city: Knoxville

first: Qiang

last: He

state: TN

address: 57A Perkins Hall

department: Civil and Environmental Engineering

institute: The University of Tennessee

summary:
In order to obtain a global view of energy metabolism pathways of the sulfate-reducer Desulfovibrio vulgaris Hildenborough and the proteins involved therein whole-genome microarrays were used to compare the transcriptional response of cells grown with hydrogen/sulfate, pyruvate/sulfate, lactate/thiosulfate, and pyruvate with limiting sulfate, relative to growth in standard lactate/sulfate condition. Growth with hydrogen/sulfate showed the largest number of differently expressed genes and the largest changes in expression levels. The most up-regulated energy metabolism genes were those coding for the periplasmic [NiFeSe] hydrogenase, followed by the Ech hydrogenase, and the most down-regulated were genes coding for the Coo hydrogenase. The results point to the involvement of formate cycling and the ethanol pathway during growth on hydrogen, whereas there is evidence for CO cycling during growth on lactate and pyruvate, but not on H2. Growth with thiosulfate showed the hallmarks of a reduced energy status of the cells with down regulation of the ATP synthase and the Qmo and Dsr complexes., whereas growth with pyruvate showed the smallest differences but an increased role for the Ech hydrogenase.that in this case functions in reverse from the case of growth with H2.
The multiple periplasmic hydrogenases and formate dehydrogenases, do not display the same regulation pattern showing that their metabolic roles are not totally interchangeable. This result together with the observation that several genes coding for proteins that have not been biochemically characterised were considerably affected in this study, reveals a more complex energy metabolism than previously considered and provides guidance for further studies.
Keywords: Growth protocol

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Desulfovibrio vulgaris Hildenborough was cultured at 37°C with thiosulfate as the only electron acceptor (with lactate as the electron donor) to mid-log phase. Cultures were also cultivated similarly using sulfate as the sole electron acceptor to mid-log phase. Gene expression profiles of cultures grown with thiosulfate as the electron acceptor were compared with those of the cultures grown with sulfate as the electron acceptor for dissimilatory sulfate reductiontion. Total RNA was harvested from four replicate cultures for microarray analysis. RNA extraction, purification, and labeling were performed independently on each cell sample. Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization (dye swap).

first: Patrícia

last: Pereira


title: Pyruvate vs Lactate as electron donor in Sulfate reduction

platform_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Desulfovibrio vulgaris Hildenborough was cultured at 37°C with pyruvate as the only electron donor (with sulfate as the electron acceptor) to mid-log phase. Cultures were also cultivated similarly using lactate as the sole electron donor to mid-log phase. Gene expression profiles of cultures grown with pyruvate as the electron donor were compared with those of the cultures grown with lactate as the electron donor for sulfate reduction. Total RNA was harvested from three replicate cultures for microarray analysis. RNA extraction, purification, and labeling were performed independently on each cell sample.Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization (dye swap).


title: Glycerol metabolism and PrfA activity in Listeria monocytogenes

status: Public on May 30 2008

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

summary:
Listeria monocytogenes is able to efficiently utilize glycerol as carbon source. In a defined minimal medium the growth rate is similar (during balanced growth) in presence of glycerol as in presence of glucose or cellobiose. Comparative transcriptome analyses of L. monocytogenes showed in the presence of glycerol (compared to glucose and/or cellobiose) high transcriptional upregulation of the known genes involved in glycerol uptake and metabolism (glpFK, glpD). Expression of the genes encoding a second putative glycerol uptake facilitator (GlpF-2) and a second putative glycerol kinase (GlpK-2) was less enhanced under these conditions. GlpK-1 but not GlpK-2 was essential for glycerol catabolism in L. monocytogenes under extracellular conditions, while loss of GlpK-1 affected replication in Caco-2 cells less than loss of GlpK-2 and GlpD. Additional genes whose transcription was higher in presence of glycerol than in presence of glucose and cellobiose included those for two dihydroxyacetone (Dha) kinases and many genes that are under carbon catabolite repression (CCR) control. Transcriptional down-regulation in the presence of glycerol (compared to glucose and cellobiose) was observed for several genes and operons that are positively regulated by glucose, including genes involved in glycolysis, N-metabolism and biosynthesis of branched chain amino acids. The highest transcriptional up-regulation was observed for all PrfA-dependent genes during early and late logarithmic growth in glycerol.  Under these conditions a low level of HPr-Ser-P and a high level of HPr-His-P was present in the cells, suggesting that all EIIA (B) components of the PTS permeases expressed will be phosphorylated. These and other data reported suggest that the phosphorylation state of PTS permeases correlates with PrfA activity.
Keywords: Response of Listeria monocytogenes to different carbon sources

overall_design: A total of four independently isolated RNA samples from each condition at each growth phase were used for the analysis. RNA from two isolations were pooled and hybridized onto two microarray slides with dye swap. Another two microarray slides were hybridized using the same principle. In total, we used four RNAs and four microarray slides to generate 16 replicate expression values for each combination except for the comparison between glucose and cellobiose, phase B where data generated from three microarray slides were used for further analysis

first: Biju

last: Joseph

first: Sonja

last: Mertins

first: Regina

last: Stoll

first: Jennifer

last: Schär

first: Kanasinakatte

last: Umesha

first: Qin

last: Luo

first: Stefanie

last: Müller-Altrock

first: Werner

last: Goebel


title: Pyruvate fermentation vs Lactate-Sulfate

overall_design: Desulfovibrio vulgaris from our laboratory culture collection was cultured at 37°C with pyruvate as the only substrate (without sulfate as the electron acceptor) to mid-log phase. Cultures were also cultivated similarly in Lactate-Sulfate medium to mid-log phase. Gene expression profiles of cultures grown under pyruvate fermentation were compared with those of the cultures grown via sulfate reduction. Total RNA was harvested from four replicate cultures for microarray analysis. RNA extraction, purification, and labeling were performed independently on each cell sample.Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization.


title: Nucleosome Mapping in S. pombe Centromeres

first: Jun

middle: S

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

type: Genome binding/occupancy profiling by genome tiling array

summary:
A key element for defining the centromere identity is the incorporation of a specific histone H3, CENP-A, known as Cnp1p in S. pombe.  Previous studies have suggested that functional S. pombe centromeres lack nucleosome arrays and may involve chromatin remodeling as a key step of kinetochore assembly.  We used tiling microarrays to show that nucleosomes are in fact positioned in regular intervals in the core of centromere 2, providing the first high resolution map of regional centromere chromatin. Nucleosome locations are not disrupted by mutations in kinetochore proteins cnp1, mis18, mis12, nuf2, mal2, overexpression of Cnp1p, or deletion of ams2.  Bioinformatic analysis of the centromere sequence indicates certain enriched motifs in linker regions between nucleosomes and reveals a sequence-bias in nucleosome positioning.  We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence.  In addition, sequence analysis of nucleosome-free regions identifies novel binding sites for the GATA-like protein Ams2p, which participates in CENP-A incorporation.
Keywords: Nucleosome Mapping Study

overall_design: Entire cnt regions and histone-related genes were tiled at 1-5 bp spacing using 60-mer probes.

first: Xingkun

last: Liu

first: Xiangwei


title: Role of M. tuberculosis dosS and dosT in CO sensing

status: Public on May 29 2008

first: Michael

last: Shiloh

institute: University of California at San Francisco

summary:
Transcriptional profiling of M. tuberculosis dosR and dosS mutants and wild type growing in log phase treated with carbon monoxide or nitric oxide versus untreated controls
Keywords: Genetic modification

overall_design: Two condition experiment, DETANO treated cells at 100 uM or CO treated cells at 20000 ppm versus untreated controls for various M. tuberculosis mutants. Biological replicates: 2 replicates per dose, 1 array per replicate

first: Jeffery

last: Cox


title: Hydrogen vs Lactate as electron donor in Sulfate reduction

overall_design: Desulfovibrio vulgaris from our laboratory culture collection was cultured at 37°C with hydrogen as the only electron donor (with sulfate as the electron acceptor) to mid-log phase. Cultures were also cultivated similarly using lactate as the sole electron donor to mid-log phase. Gene expression profiles of cultures grown with hydrogen as the electron donor were compared with those of the cultures grown with lactate as the electron donor for sulfate reduction. Total RNA was harvested from four replicate cultures for microarray analysis. RNA extraction, purification, and labeling were performed independently on each cell sample.Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization (dye swap).


title: Comparison of ES vs EB cells

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

institute: Institute for Molecular Bioscience, Uni of Qld

summary:
Direct pairwise comparison of Mouse ES and Mouse Embryonic Day 4 cells
Keywords: Direct pairwise comparison

overall_design: Pairwise comparison of 2 samples utilising the Illumina bead array platform


title: Gene regulation in ES cell lines with different nuclei donor cell sources

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary:
Comparison of ES cell line of different genetic background and different cloning methods to identify changes on gene expression levels between these ES cell lines. The main question behind the experiments id, if there is major/important difference on gene expression level between NT embryo-derived ES cell liens and control embryo derived ES cell lines. Ih has an effect on therapeutic cloning that means the nuclei donor cell source could be an important question. We also included different genetic background cell lines (HM-1 is 129/SV, #4 ES cell line is B6D2F1 derived heterozygote cell line) to compare the effect of gentic background differences. Hetero- and homozygosis con be compared based on the PGA ES cell line from the same genetic backgound.
Keywords: cDNA microarray, murine ES cells, nucleous transfer

overall_design: 13 comparisons of different ES cell lines with different nuclei donor cell sources. For each sample comparison 4 chip experiments were performed including 2 dye swaps. Two ES cell lines derived from cumulus nuclei donor cells but differetn cloning methods was used to produce the embryos

first: Johannes

last: Becker

first: Marion

last: Horsch

first: Andras

last: Dinnyes


title: Discovery of the targets of the immune response to chronic myeloid leukemia in 3 patients using protein microarrays

first: Ovidiu

last: Marina

summary:
Three patients who had relapsed chronic myeloid leukemia after allogeneic bone marrow transplant and received an immunotherapeutic intervention (donor lymphocyte infusion, or DLI) without further treatment were studied. The binding of serum immunoglobulins to proteins after immunotherapy was compared to before in two patients using Invitrogen ProtoArrays from a single lot. For a third patient, comparison was made between two timepoints after immunotherapy against one timepoint before using Invitrogen ProtoArrays from a separate lot. Significant interactions were determined by comparing each after sample separately against the before sample from that patient, using the Concentration-Dependent Analysis described in Marina et al., J Proteome Res, 2008. The goal was to identify proteins with significantly-increased reactivity after donor lymphocyte infusion.

Keywords: Immune response discovery

overall_design: One sample from before and one sample from after immunotherapy were tested for 2 patients, and one sample from before and two samples from after immunotherapy were tested for a third patient.


title: Steptoe x Morex seedling leaf comparison

status: Public on May 27 2008

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

summary:
This study was to collect expression level polymorphism (ELP) data for the barley genotypes Steptoe and Morex, parents of a widely used North American mapping population.  Primarily, the data collected will show the amount of variation between these genotypes in seedling leaves grown in a greenhouse at the same time, with replications on three separate dates.
-----------------------------------------------------------------------------------------------------------------------
Roger P. Wise(Head of Lab) and Stacy Barkeloo are the original contributors of this experimental data.  PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of them .  The equivalent experiment is 'BB16' at PLEXdb.
Keywords: genotype

overall_design: genotype: Steptoe(3-replications);  genotype: Morex(3-replications)

first: Stacy

last: Barkeloo

first: Roger

middle: P

last: Wise


city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

type: Genome variation profiling by genome tiling array

summary:
Array-CGH analysis of X chromosome of XLMR patient
Keywords: comparative genomic hybridization

overall_design: Comparison of 6 patient samples in 2 dyes; samples XY1, Xy2, and XY3 can be considered as control samples.

first: Guy

last: Froyen

first: Paul

last: Van Hummelen


title: response of Escherichia coli and glutathion mutants to Cadmium

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

summary: We investigated the impact of cadmium on the global transcriptome of E. coli wild type, ∆gshA and ∆gshB mutant cells to evaluate the molecular basis of cadmium toxicity in the presence or absence of cellular thiols. This global transcriptome analysis were done with cells synthezising GSH (wild type), gamma-glutamyl-cysteine (∆gshB mutant) or neither of the two cellular thiols (∆gshA mutant) under the influence of 100 µM Cd(II).

overall_design:
E. coli cells, wild type, ∆gshA and ∆gshB mutant strain, were grown at 37 °C . At a cell turbidity of 100 Klett, cells were treated for 10 min with 100 µM Cd(II) or no metal as a control in TMM medium.
Total RNA was extracted, DNAse digested and reverse-transcribed with either Cy3- or Cy5-labeled dCTP. Both labeled cDNA were hybridized to a slide at 42 °C. All experiments were performed with three independent biological repeats.

first: Kerstin

last: Helbig

first: Dietrich

last: Nies


title: Expression responses of lineage I and II Listeria monocytogenes strains to low pH and sodium diacetate

city: Hobart

first: John

middle: Phillip

last: Bowman

state: Tasmania

address: College Road, Sandy Bay

department: School of Agricultural Science

institute: University of Tasmania

summary: Cultivation based analyses were used to determine the resistance of a set of 140 Listeria monocytogenes strains to weak organic acids. Strains of lineage I tended to exhibit greater overall resistant to four different organic acids compared to lineage II strains. Resistant strains also possessed higher survival levels following challenge to pH 2.4 compared to sensitive strains. Transcriptomic analyses were performed to determine genetic responses relevant to growth at mildly acidic conditions (pH 5.0) and to the presence of sodium diacetate. Lineage I and II strain representatives, clinical strain ATCC 19115 and food isolate FW04/0023, were found to exhibit similar transcriptomic changes when habituated to pH 5.0 in brain heart infusion broth (BHIB) relative to growth at pH 7.2 though considerably more divergent responses were detected when 21 mM sodium diacetate was present. Homogeneity in acid habituation-related gene expression was reflected in relatively homogenous SigB, PrfA, HrCA and CodY regulon expression responses. In the presence of sodium diacetate, SigB and PrfA regulon genes found to be upregulated in sigB and prfA null mutants were overall repressed but SigB dependent-gene activation was not evident. L. monocytogenes strains responses to sodium diacetate were observed in different expression trends amongst various functionally-related gene sets and in particular the expression of the PrfA, Atp, Kdp, Cob, Pdu, Eut and Dlt operons; iron transporter and heat shock-related proteins. The results suggest there is diversity in the specific responses to weak organic acids and subsequent cytosolic acidification amongst L. monocytogenes strains though the acid tolerance response itself manifests as a more conserved set of expression responses.

overall_design:
Strain ATCC 19115, pH 5.0 vs. pH 7.2, two biological replicates, each with 2 technical replicates
Strain FW040023, pH 5.0 vs. pH 7.2, two biological replicates, each with 2 technical replicates
Strain ATCC 19115, pH 5.0+sodium diacetate vs. pH 5.0, two biological replicates, each with 2 technical replicates
Strain FW040023, pH 5.0+sodium diacetate vs. pH 5.0, two biological replicates, each with 2 technical replicates

first: Jye

middle: L

last: Chang

first: Rolf

last: Nilsson

first: Tom

last: Ross


title: Efficient targeted transcript discovery via array-based normalization of RACE libraries

status: Public on May 25 2008

city: Santa Clara

first: Thomas

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

type: Expression profiling by genome tiling array

summary: RACE (Rapid Amplification of cDNA Ends) is a widely used approach for transcript identification. However, the dynamic range in the population of RACE transcript isoforms may be very large, and random clone selection -the typical approach- may be ineffective in sampling the different transcript species present in the population. Here, we describe an effective RACE sampling strategy. The products of the RACE reaction are hybridized onto high-density tiling arrays, and the exons detected are then used to delineate a series of RT-PCR reactions, through which the original RACE mixture is segregated into a number of simpler RT-PCR reactions. These are independently cloned, and randomly selected clones are sequenced. This approach is superior to the direct cloning and sequencing of the RACE products: it specifically targets novel transcripts, and often leads to the overall normalization of their abundances. We indeed show theoretically that this strategy leads to a very efficient sampling of the novel transcript species associated to annotated loci. In a pilot experiment, we used this approach to discover many novel transcripts for a few otherwise well-characterized protein coding genes. Finally we investigate how this strategy can be multiplexed for large-scale transcript discovery by high-density pooling of RACE reactions prior to hybridization. Our results indicate that through the interrogation of a limited number of exons per gene on a limited number of cell types, it is possible to recover a large fraction of the transcript diversity associated to protein coding loci. These loci, however, could be occupying a much larger genomic space than previously expected, implying that efficient multiplexing requires non-trivial pooling optimization.

overall_design:
Question-1 (Q1 Samples): To uncover the ideal number and choice of tissues to get the best coverage of transcription (both annotated and newly-identified exons), we performed 5'- and 3' RACEs of 12 genes on polyA+ RNAs from 48 different cell/tissue types, i.e. 33 human adult tissues (Adrenal Gland, Bladder, Brain, Brain Frontal Lobe, Brain Hippocampus, Brain Hypothalamus, Cerebellum, Colon, Epididymus, Heart, Kidney, Liver, Lung, Lymph Node, Mammary Gland, Muscle, Ovary, Pancreas, Pituitary Gland, Placenta, Prostate, Salivary Gland, Skin, Small Intestine, Spinal Cord, Spleen, Stomach, Testis, Thymus, Thyroid, Tongue, Tonsil, Uterus; all BD Clontech), 9 fetal tissues (Fetal Adrenal Gland, Fetal Brain, Fetal Heart, Fetal Kidney, Fetal Liver, Fetal Lung, Fetal Spleen, Fetal Thymus, Whole Fetus; all BD Clontech) and 6 cell lines (GM06990, HeLaS3, HepG2, HL60, K562, SW480) using the BD SMARTTM RACE cDNA amplification kit (BD Clontech Cat. No.634914). Overall: 96 experiments representing two pools of 6 genes done in the 48 samples separately.

Question-2 (Q2 Samples): To define how many exons per gene should be interrogated, we performed 5'RACE experiments in ten exons of a set of 44 genes, each mapping to a different ENCODE region15,23 on polyA+ RNAs from 12 tissues (brain, heart, kidney, spleen, liver, colon, small intestine, muscle, lung, stomach, testis, placenta, all BD Clontech). Overall: 120 experiments representing 10 pools each with RACE reactions from a separate exon of the 44 genes done in the 12 samples separately.

Question-3 (Q3 Samples): The same set of 12 RNAs and 5'RACE of 96 genes mapping to HSA21 and HSA22 was used to estimate the genomic space occupied by a gene. Overall: 16 experiments representing 16 pools of 6 genes each done on a pool of 12 samples.


title: Dose response of carbon monoxide treatment of M. tuberculosis

first: Michael

last: Shiloh

summary:
Transcriptional profiling of M. tuberculosis growing in log phase treated with various concentrations of carbon monoxide versus untreated controls
Keywords: Dose response

overall_design: Two condition experiment, CO treated cells at 2000, 200 and 20 ppm versus untreated controls. Biological replicates: 2 replicates per dose, 1 array per replicate

first: Jeffery

last: Cox


status: Public on May 24 2008

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

country: China

institute: Institute of plant physiology & ecology, SIBS, CAS

summary:
Expression profiles of MicroRNA and SiRNA of Arabidopsis thaliana Col-0 and transgenic plants with constitutive expression of the chimeric receptors NRG1 grown at different temperature
To reveal the underlying molecular mechanism of de-cosuppression with memory by high temperature in Arabidopsis, we performed the expression profiles of microRNA and SiRNA in transgenic plants with constitutive expression of the chimeric receptors NRG1 and wide type Col-0 grown at different temperature using the Custom LC Sciences Arabidopsis microRNA and SiRNA array.

Keywords: high temperature, de-cosuppression, MicroRNA, SiRNA

overall_design: Total RNA was prepared from wild type and NRG1 plants grown at 22ºC and 30ºC for 4 weeks with TRIzol reagent according to the manufacturer’s protocol (Invitrogen). Small RNAs (<300nt) were isolated using a YM-100 Microcon centrifugal filter (Millipore), and 3’-extended with a poly(A) tail for later fluorescent dye staining. Two different tags were used for the two RNA samples labeled with Cy3 or Cy5 fluorescent dyes in dual-sample experiments. Also dye-swap experiments were carried out to control for labeling bias. Hybridization was performed overnight on a µParafloTM microfluidic chip. Each miRNA and siRNA had 6 and 3 repeat prints, respectively. Six replicate arrays were performed with six independent pairs of RNA samples. After hybridization, array images were obtained using an Axon GenePix 4000B laser scanner and digitized using the Array-Pro image software (Media Cybernetics). The data were corrected by subtracting the background and normalized using the LOWESS (locally weighted regression) method. All data calculations were performed by LC Science (Houston, TX).

first: Sihui

last: Zhong

first: Qun

last: Li

first: Zuhua

last: He


title: Nuclear Localization of Hog1 MAPK is Not Necessary for Resistance to Hyperosmotic Stress

city: Berkeley

first: Jesse

middle: C

last: Patterson

address: 528 Barker Hall

department: Dept of Molecular and Cell Biology

institute: UC-Berkeley

summary:
In budding yeast, this signaling pathway—  the high-osmolarity glycerol (HOG) response  —culminates in dual phosphorylation and nuclear translocation of the MAPK, Hog1 (ortholog of mammalian p38/SAPK).  Induction of at least 50 genes requires nuclear Hog1, implying that transcriptional up-regulation is necessary to cope with hyperosmotic stress.  Contrary to this expectation, we found that cells lacking the karyopherin (Nmd5) required for Hog1 nuclear import or in which Hog1 was permanently anchored at the plasma membrane(HOG1-CCAAX) (or both) withstood hyperosmotic challenge by three different solutes (1 M sorbitol, KCl or NaCl).  In cells where activated Hog1 is excluded from the nucleus, there was little change in transcriptional program after exposure to hyperosmotic shock (comparable to hog1∆ cells), as judged by examining several diagnostic mRNAs and by global transcript measurements using microarrays.  Systematic genetic analysis ruled out the need for any transcription factor known to be influenced by Hog1 (Hot1, Msn2, Msn4, Sko1 and Smp1).
Keywords: Time course of stress response gene expression array

overall_design:
The transcriptomes' of HOG1-GFP, hog1del, and HOG1-CCAAX strains before and after 60 min hyperosmotic shock with 1M sorbitol at 25C were compared.  Three biological replicates were done, with the first biological replicate done in technical triplicate, and the final two biological replicates beind done in technical duplicate by in slide duplication of features.

Several supplementary files attached to the Series are summarized below:
GSE8703 B1, B2, B3 Tscombined_matrix files show the averages of the technical replicates for each biological replicate.
GSE8703 B1, B2, B3 norm_to_0_matrix files show the fold change over the time course (log2 time 60 - log2 time 0) for each of the three strains in each biological replicate.
GSE8703 Figure_S6 shows the 30 genes with the most significant difference between the HOG1-GFP strain and the hog1del strain as determined by SAM. Genes were identified as: >3 fold induction in HOG1-GFP over 60 minute hyperosmotic shock and <3 fold induction in hog1del over 60 minute hyperosmotic shock.

first: Patrick

last: Westfall

first: Raymond

middle: E

last: Chen

first: Jeremy

last: Thorner


title: Mll5 is Required for Hematopoietic Stem Cell Fitness and Homeostasis

status: Public on May 22 2008

first: Yan

last: Zhang

address: 513 Parnassus Ave, HSE1001B

department: Microbiology and Immunology

institute: University of California, San Francisco

summary:
MLL5 is a novel trithorax group gene and a candidate tumor suppressor gene located within a 2.5 Mb interval of chromosome band 7q22 that is frequently deleted in human myeloid malignancy.  Here we show that Mll5 is required for normal hematopoietic stem cell (HSC) homeostasis. Inactivation of the Mll5 gene in mice results in reduced cellularity of the long-term HSC compartment, which correlates with functional impairment of long-term repopulation potential under competitive conditions.  Bone marrow cells from Mll5-deficient mice were defective in spleen colony-forming assays, and the mutant mice showed enhanced susceptibility to 5-Fluorouracil-induced myelosuppression.  Heterozygous and homozygous Mll5 mutant mice did not spontaneously develop hematologic cancers, and loss of Mll5 did not alter the phenotype of a fatal myeloprolferative disorder induced by oncogenic Kras in vivo.  Collectively, the data reveal an important role for Mll5 in HSC homeostasis, and provide a basis for further studies to explore its role in leukemogenesis.
Keywords: Cell type comparision.

overall_design:
Global gene expression analysis.

Bone marrow cells were pooled from 6 pairs of eight weeks old Mll5-/- mice and sex matched wild type littermates, and then were stained with a cocktail of biotinylated anti-mouse lineage antibodies to CD3, CD4, CD5, CD8, B220, CD11b, Gr-1 and Ter119 (eBioscience). For detection and sorting, we used Streptavidin conjugated with PE-Cy7, anti-Sca-1-APC and c-Kit-APC-Alexa F750 antibodies (eBioscience). 2.5 × 105 LSK (Lin-, Sca-1+, c-kit+) cells were flow sorted. Total RNA (320 ng) was isolated by using RNeasy Mini kit (Qiagen) following the manufactures instruction. RNA amplification and array hybridization were performed in UCSF Shared Microarray Core Facilities. Briefly, total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent). Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hours, according to the manufacturers protocol (Agilent). Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent,).

first: Mark

last: Klinger

first: Nigel

last: Killeen


title: Mutual Antagonistic Relationship Between Prostaglandin E2 and Interferon-(gamma): Implications for Rheumatoid Arthritis

city: Kirkland

first: Alex

middle: G.

last: Therien

address: 17611 Transcanada Hwy.

department: Biochemistry and Molecular Biology

institute: Merck Frosst Canada, Ltd.

summary: PGE2 is a major mediator of inflammation and is present at high concentrations in the synovial fluid of rheumatoid arthritis (RA) patients.  PGE2, acting through the EP4 receptor, has both pro- and anti-inflammatory roles in vivo. To shed light on this dual role of PGE2, we investigated its effects in whole blood and in primary human fibroblast-like synoviocytes. Gene expression analysis in human leukocytes, confirmed at the protein level, revealed an EP4-dependent inhibition of the expression of genes involved in the IFN-gamma activation pathway, including IFN-gamma itself. This effect of the PGE2/EP4 axis on IFN-gamma is a reciprocal phenomenon since IFN-gamma blocks PGE2 release and blocks EP receptor expression. The mutually antagonistic relationship between IFN-gamma and PGE2 extends to downstream cytokine- and chemokine-release; PGE2 counters the effects of IFN-gamma, on the release of IP-10, IL-8, TNFalpha and IL-1beta. To gain further insight into IFN-gamma-mediated cellular events in rheumatoid arthritis, we assessed the effects of IFN-gamma on gene expression in fibroblast-like synoviocytes. We observed an IFN-gamma-dependent up-regulation of macrophage-attracting chemokines, and down-regulation of metalloprotease expression. These results suggest the existence of a mutually antagonistic relationship between PGE2 and IFN-gamma which may represent a fundamental mechanism of immune control in diseases such as RA.

overall_design: For details, see Mathieu MC et al, EJI, issue 7, 2008

first: Marie-Claude

last: Mathieu

first: Simon

last: Lord-Dufour

first: Virginie

last: Bernier

first: Yves

last: Boie

first: Jason

last: Burch

first: Patsy

last: Clark

first: Danielle

last: Denis

first: Yongxin

last: Han

first: James

last: Mortimer

middle: G


title: Expression QTL mapping of Toxoplasma gondii genes, Tachyzoite array

city: Stanford

first: Jon

last: Boyle

address: 299 Campus Drive

institute: Stanford University School of Medicine

summary:
Toxoplasma gondii is an intracellular parasite with a significant impact on human health, especially in cases where individuals are immunocompromised (e.g., due to HIV/AIDS).  In Europe and North America only a few clonal genotypes appear to be responsible for the vast majority of Toxoplasma infections, and these clonotypes have been intensely studied to identify strain-specific phenotypes that may play a role in the manifestation of more severe disease.  To identify and genetically map strain-specific differences in gene expression, we have carried out expression quantitative trait locus (eQTL) analysis on Toxoplasma gene expression phenotypes using spotted cDNA microarrays.  This led to the identification of 16 Toxoplasma genes that had significant and mappable strain-specific variation in hybridization intensity.  While the analysis should identify both cis and trans-mapping hybridization profiles, we only identified loci with strain-specific hybridization differences that are most likely due to differences in the locus itself (i.e., cis-mapping).  Interestingly, a larger number of these cis-mapping genes than would be expected by chance encode either confirmed or predicted secreted proteins, many of which are known to localize to the specialized secretory organelles characteristic of members of the phylum Apicomplexa.  For 6 of the cis-mapping loci we determined if the strain-specific hybridization differences were due to true transcriptional differences or rather strain-specific differences in hybridization efficiency because of extreme polymorphism and/or deletion, and we found examples of both scenarios.

Keywords: eQTL mapping; virulence; Toxoplasma gondii

sample_organism:
Toxoplasma gondii
synthetic construct

overall_design: 19 F1 progeny from a cross between a type II parent (PDS) and a type III parent (CTG) were used in RNA hybridizations to identify cis and trans-mapping loci regulating gene expression

first: Jeroen

last: Saeij

first: John

last: Boothroyd


title: Expression QTL mapping of Toxoplasma gondii genes, Bradyzoite array

summary:
Toxoplasma gondii is an intracellular parasite with a significant impact on human health, especially in cases where individuals are immunocompromised (e.g., due to HIV/AIDS).  In Europe and North America only a few clonal genotypes appear to be responsible for the vast majority of Toxoplasma infections, and these clonotypes have been intensely studied to identify strain-specific phenotypes that may play a role in the manifestation of more severe disease.  To identify and genetically map strain-specific differences in gene expression, we have carried out expression quantitative trait locus (eQTL) analysis on Toxoplasma gene expression phenotypes using spotted cDNA microarrays.  This led to the identification of 16 Toxoplasma genes that had significant and mappable strain-specific variation in hybridization intensity.  While the analysis should identify both cis and trans-mapping hybridization profiles, we only identified loci with strain-specific hybridization differences that are most likely due to differences in the locus itself (i.e., cis-mapping).  Interestingly, a larger number of these cis-mapping genes than would be expected by chance encode either confirmed or predicted secreted proteins, many of which are known to localize to the specialized secretory organelles characteristic of members of the phylum Apicomplexa.  For 6 of the cis-mapping loci we determined if the strain-specific hybridization differences were due to true transcriptional differences or rather strain-specific differences in hybridization efficiency because of extreme polymorphism and/or deletion, and we found examples of both scenarios.
Keywords: eQTL mapping; virulence; Toxoplasma gondii

overall_design: 17 F1 progeny from a cross between a type II parent (PDS) and a type III parent (CTG) were used in RNA hybridizations to identify cis and trans-mapping loci regulating gene expression


title: Gene expression of E. coli MG1655 wild type and rpoS knock-out strains

status: Public on May 23 2008

city: Sapporo

first: Akinobu

last: Ito

address: North-13, West-8, Kitaku

department: Graduate School of Engineering

country: Japan

institute: Hokkaido University

summary:
The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). Genes involved in the energy metabolism and the flagella synthesis showed higher expression in the rpoS knock-out biofilms (MBF), but not in the wild type biofilms (WBF). Moreover, genes involved in the stress responses showed higher expression in the wild type biofilms (WBF), but not in the rpoS knock-out biofilms (MBF).
Keywords: cell type comparison (biofilms vs planktonic cells, wild type vs rpoS knock-out strains)

overall_design: Affymetrix E. coli antisense genome array was used to compare the gene expression among E. coli wild type and rpoS konck-out strains in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. All samples were grown in MOPS minimal media with 0.2% glucose. Biofilms were grown for 72 hours on glass surface in flow cells (1x4x40 mm), and planktonic cells were grown for 8 hours (exponential phase) and 12 hours (stationary phase). Experiments were repeated 3 times, which resulted in 3 replicates of 6 different samples.

first: Thithiwat

last: May

first: Koji

last: Kawata

first: Satoshi

last: Okabe


title: High expression of SerpinA1 and SerpinA3 in HLA-positive cervical cell carcinomas

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

institute: Leiden University Medical Center

summary:
In cervical cancer, an important mechanism by which tumour cells escape immune surveillance is loss of HLA class I, enabling tumours to evade recognition and lysis by cytotoxic T lymphocytes. Some tumours, however, escape from immune surveillance without accumulating defects in antigen presentation. We hypothesized that tumours with no or partial loss of HLA class I develop alternative mechanisms to prevent immune surveillance. To investigate this hypothesis, genome-wide expression profiling using Illumina arrays was performed on cervical squamous cell carcinomas showing overall loss of HLA class I, partial and normal HLA class I protein expression. Statistical analyses revealed no significant differences in gene expression between tumours with partial (n = 11) and normal HLA class I expression (n = 10). Comparison of tumours with normal/partial HLA class I expression (n = 21) with those with overall loss of HLA class I expression (n = 11) identified 150 differentially expressed genes. Most of these genes were involved in the defense response (n = 27), and, in particular, inflammatory and acute phase responses. Especially SerpinA1 and SerpinA3 were found to be upregulated in HLA positive tumours (3.6 and 8.2 fold, respectively), and this was confirmed by real-time PCR and immunohistochemistry. In a group of 117 tumours, high SerpinA1 and SerpinA3 expression in association with normal/partial HLA expression correlated significantly with poor overall survival (p = 0.035 and p = 0.05, respectively). This study shows that HLA positive tumours are characterized by a higher expression of genes associated with an inflammatory profile and that expression of the acute phase proteins SerpinA1 and SerpinA3 in HLA positive tumours is associated with worse prognosis.
Keywords: Cell type comparison

overall_design: Formalin-fixed, paraffin-embedded squamous cervical carcinomas from 68 patients who underwent radical hysterectomy with bilateral lymphadenectomy between 1991 and 2005 at Leiden University Medical Center, were collected. From these 68 patients, 32 snap-frozen tissues were chosen for subsequent gene expression profiling. The percentage of tumour cells was estimated by visual examination of HE-stained frozen tissue sections (5 μm). Only tissue blocks with areas that contained at least 60% viable tumour cells were selected. The 32 selected tumours were divided in three groups: group A, tumours with less than 5% or no HLA class I positive tumour cells (n = 11); group B, tumours with no or partial loss of HLA class I expression and LOH at 6p21.3 (n = 11); and group C, tumours with normal HLA class I expression and no LOH at 6p21.3 (n = 10). Group C included 5 cases with minimal loss, defined as weak expression of HLA-A or HLA-B/C. Statistical analysis revealed no differentially expressed genes between group B and C. Only 15 genes were significantly differentially expressed between group A and B, and 15 genes between group A and C. Since no differences in gene expression were observed between the groups with HLA expression (B and C), we combined the samples of group B and C into one group. Overall, 150 genes were significantly differentially expressed between the HLA negative group (group A, n = 11) and the HLA positive group (group B/C, n = 21)

first: Judith

last: Kloth

first: Arko

last: Gorter

first: Ekaterina

last: Jordanova

first: Sandra

last: Uljee

first: Natalja

last: ter Haar

first: Enno

last: Dreef

first: Gemma

last: Kenter

first: Gert-Jan

last: Fleuren


title: Comparison of gene expression between A549 and WI38VA13

status: Public on May 21 2008

city: Gyeongju-si

first: Kyung-Oh

last: Doh

state: Gyeongsangbuk-do

address: 707 Seokjang-dong

department: Physiology

country: South Korea

institute: Dongguk University

summary:
Gene expression profile of A549 and WI38VA13 was compared.
Keywords: cell type comparison

overall_design: Total RNA of one sample from each cell lines was analyzed

first: Yun-Han

last: Lee

first: Seok-Yong

last: Uhm

first: Ik-Jae

last: Moon

first: Jong-Gu

last: Park


title: Identification of transcriptional changes due to loss of Hdac3 in liver at P17 and P28

city: Nashville

first: Sarah

last: Knutson

address: 23rd and Pierce Ave

department: Biochemistry

institute: Vanderbilt University

summary:
Histone deacetylase 3 (Hdac3) is the enzymatic component of transcriptional repression complexes recruited by the nuclear hormone receptors.  Inactivation of Hdac3 in cancer cell lines triggered apoptosis, and removal of Hdac3 in the germ-line of mice caused embryonic lethality.  Therefore, we conditionally deleted the Hdac3 allele in the mouse liver.  These mice developed hepatomegaly, which was the result of hepatocyte hypertrophy, and these morphological changes coincided with significant imbalances between carbohydrate and lipid metabolism.  Loss of Hdac3 triggered changes in gene expression consistent with inactivation of repression mediated by nuclear hormone receptors.  Mechanistically, loss of Hdac3 increased the levels of Pparγ2, and treatment of these mice with a Pparγ antagonist partially reversed the lipid accumulation in the liver.  In addition, gene expression analysis identified mTOR (mammalian target of rapamycin) signaling as being activated by deletion of Hdac3, and inhibition by rapamycin also affected the accumulation of neutral lipids in the Hdac3-null livers.  Thus, Hdac3 has a key role in regulation of multiple signaling pathways in the liver, and deletion of Hdac3 disrupts normal metabolic homeostasis.
Keywords: Genetic knockout of Hdac3 specifically in liver, and RNA analyzed from postnatal day 17 or 28 livers for transcriptional changes related to the given phenotypes

overall_design: Postnatal day 17 or 28 mice were used for the microarray analysis.  Total RNA was extracted from livers of either Hdac3 wild-type/heterozygous mice expressing Albumin-Cre or Hdac3-null livers, and pooled together in groups of 5.  One pool of control or Hdac3-null liver RNA from both time points was used in technical replicates, meaning each sample was run in duplicate on separate lots of microarray chips to determine reproducibility of the Applied Biosystems ABI1700 chips.  The second set of RNA pools were used as biological replicates for each group at each time point.

first: Brenda

last: Chyla

first: Joseph

middle: M

last: Amann

first: Srividya

last: Bhaskara

first: Stacey

last: Huppert

first: Scott

middle: W

last: Hiebert


title: Mechanism for Fe(III) Reduction in Pelobacter carbinolicus

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

summary:
Pelobacter carbinolicus is phylogenetically intertwined with the Geobacteraceae, a family of deltaproteobacteria which couple oxidation of organic compounds to Fe(III) reduction.  Whereas Geobacter species completely oxidize organic compounds to CO2, Pelobacter species either ferment or oxidize short chain alcohols to acetate.  Pelobacter species also contain far fewer c-type cytochromes, proteins which play a role in electron transfer during Fe(III) respiration,  compared to their Geobacter counterparts.
Keywords: two-condition comparison

overall_design: Three biological replicates were hybridized in duplicate.  Experimental (FeIII) was labeled with cy5, control (acetoin) was labeled with cy3.

first: Shelley

middle: A

last: Haveman


title: Gene Profiling in the Livers of Wild-Type and PPARalpha-Null Mice Exposed to Perfluorooctanoic Acid (PFOA)

city: Research Triangle Park

first: Mitchell

middle: B

last: Rosen

state: NC

department: Reproductive Toxicology

institute: U.S. EPA

summary:
Unlike the PPARalpha agonist W14,643, PFOA is capable of inducing effects independently of PPARa. Genes altered in the PPARalpha-null mouse following exposure to PFOA included those associated with fatty acid metabolism, inflammation, xenobiotic metabolism, and cell cycle progression. The specific signaling pathway(s) responsible for these effects is not readily apparent but it is conceivable that other members of the nuclear receptor superfamily such as PPARbeta/delta and CAR may be involved.
Keywords: dose response

overall_design: Wild-type and PPARa-null mice were orally dosed for 7 days with either PFOA (1 or 3 mg/kg), the PPARalpha agonist WY-14,643 (50 mg/kg), or compound vehicle. Gene profiling analysis was conducted on 4 animals per group using Applied Biosystems Mouse Genome Survey Microarrays.

first: Barbara

middle: D

last: Abbott

first: Douglas

last: Wolf

first: J

last: Corton

first: Carmen

last: Wood

first: Judith

last: Schmid

first: Kaberi

last: Das

first: Robert

last: Zehr

first: Eric

middle: T

last: Blair

first: Christopher

last: Lau


title: Static, aerobic, and respiratory transcriptomes of Lactococcus lactis

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

summary:
Compare the physiological state between static, aerobic, and respiratory growth of Lactococcus lactis subsp. lactis CHCC2862 using whole genome transcriptomes. NOTE: the biological replicate array GSM243206 is dye-swapped relative to GSM202337 (unlike the two other biological replicate arrays GSM243203 and GSM24205).
Keywords: Physiological response to aerobic and respiratory growth relative to static.

overall_design: Static stationary cultures of CHCC2862 (Chr. Hansen Culture Collection, Hørsholm, Denmark) were inoculated into fresh pre-heated medium at the relevant conditions. OD600 was followed over time. At OD 1.0 samples were harvested for RNA isolation.

first: Christel

last: Garrigues

first: Henrik

last: Møllgaard

first: Karin

last: Vido

first: Karine

last: Tuphile

first: Philippe

last: Gaudu

first: Alexandra

last: Gruss


title: Transcriptional analysis of wild-type Leishmania species between both stages using full-genome DNA microarrays

status: Public on May 28 2008

city: Quebec

last: Papadopoulou

state: Quebec

address: 2705 boulevard Laurier

institute: Centre de Recherche du CHUL

summary:
Transcriptional analyses of L. infantum promastigote compared to L. infantum intracellular amastigote, and  L. major promastigote compared to L. major intracellular amastigote
The full-genome DNA microarray includes one 70mer-oligonucleotide probe for each gene of L. infantum and for each gene of L.major LV39

Keywords: stage-specific comparison

sample_organism:
Leishmania major
Leishmania infantum

overall_design:
Leishmania infantum: Two-condition experiment, promastigote stage vs amastigote stage. Six biological replicates for each stage, independently grown and harvested. One replicate per array
Leishmania major: Two-condition experiment, promastigote stage vs amastigote stage. Four biological replicates for each stage, independently grown and harvested. One replicate per array

first: A

last: Rochette

first: F

last: Raymond

last: Ubeda

first: N

last: Messier

first: S

last: Boisvert

first: M

last: Smith

first: P

last: Rigault

last: Corbeil

last: Ouellette

first: B


title: The Hyphal Associated Adhesin and Invasin Als3 of Candida albicans Mediates Iron Acquisition from Host Ferritin

status: Public on May 20 2008

city: Jena

first: Bernhard

last: Hube

address: Beutenbergstr. 11a

institute: Hans Knoell Institute

summary: Iron sequestration by host iron-binding proteins is an important mechanism of resistance to microbial infections. Inside oral epithelial cells, iron is stored within the ferritin, and is therefore usually not accessible to pathogenic microbes. We observed that the ferritin concentration within oral epithelial cells was directly related to their susceptibility to damage by the human pathogenic fungus Candida albicans. Thus, we hypothesized that host ferritin may be used as an iron source by this organism. A screen of C. albicans mutants lacking components of each of the three iron acquisition systems revealed that only the reductive pathway is involved in iron utilization from ferritin by this organism. Transcriptional profiling of wild-type and hyphal-defective C. albicans strains suggested that the C. albicans invasin-like protein Als3 plays a role in ferritin binding.

overall_design: Total RNA from wild-type (CAI4) and hyphal-defective C. albicans strains (deltaHGC1, deltaRAS1) was prepared after growth under iron-limiting conditions. Each strain was labeled and compared to a common control (C. albicans strain SC5314) in four independent experiments including two dye swaps.

first: Ricardo

middle: S

last: Almeida

first: Sascha

last: Brunke

first: Antje

last: Albrecht

last: Thewes


title: Gene expression profiles of high and low immune responder Holstein cows

status: Public on May 16 2008

city: Guelph

first: Maria

middle: Isabel

last: Nino-Soto

state: Ontario

address: College Ave. West

department: Pathobiology

institute: University of Guelph

summary:
The study explores the genetic basis of high or low antibody (Ab) and cell (DTH)-mediated immune responses in Canadian Holstein cows using microarray hybridization to an in-house immune-endocrine cDNA microarray
Keywords: immune response comparison

overall_design: The study uses a common reference design for the microarray hybridizations. There are three biological replicates per group and there are four groups: high-Ab, low-Ab, high-DTH and low DTH. The design included four technical replicates with dye swap for each biological replicate.

middle: I

first: Kathleen

last: Thompson

first: Bonnie

last: Mallard


title: Pectobacterium atrosepticum host extract induced gene expression study

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

summary:
Effects of potato tuber and stem extracts on P atrosepticum gene expression

Keywords: gene expression

overall_design: 3-condition experiment, minimal medium vs tuber/stem extract, 2 biological replicates per each condition and 2 technical replicates for minimal medium and tuber samples

first: Laura

last: Mattinen

first: Minna

last: Pirhonen


title: Expression of Cell Cycle related genes in developing mouse cerebellum

status: Public on May 19 2008

city: Bologna

first: Elisabetta

last: Ciani

address: P.zza Porta San Donato, 2

department: Human and General Physiology

institute: University of Bologna

summary:
The goal of the study was to analize expression of cell cycle related genes during postnatal development of Ts65Dn (Down syndrome mouse model) and control mice cerebellum.
Keywords: Gene expression study in mouse model of disease

overall_design: RNA from 3 controls and 3 Ts65Dn postnatal day 2 cerebellum were analized on separate arrays.

first: Andrea

last: Contestabile

first: Tatiana

last: Fila

first: Renata

last: Bartesaghi


title: Spneu D39 wildtype grown in GM17 versus GM17 + 0.25 mM ZnSO4

status: Public on May 17 2008

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

summary:
This study addresses the response of Streptococcus pneumoniae to zinc. The wild-type strain D39 was grown in GM17 and GM17 with 0.25 mM of ZnSO4. The transcriptome under these conditions was compared by using microarrays.
Keywords: transcriptome analysis of D39 wild-type compared with its isogenic glnPA double mutant

overall_design:
The wild-type strain D39 was grown in 4 biological replicates in GM17 and in GM17+0.25 mM ZnSO4 to an Optical Density at 600 nm of 0.3. From these cultures samples were prepared for transciptome determination with in-house printed microarrays covering the genomes of several S. pneumoniae species. The GM17 samples (CH1) and GM17+ZnSO4 samples (CH2) were labeled with Cy5 or Cy3. Samples were hybridized to glass-microarray slides. This work is part of a publication that is likely to be released in june/july 2008: 'Opposite effects of Mn2+ and Zn2+ on the PsaR-mediated expression of the virulence genes pcpA, prtA and psaBCA of Streptococcus pneumoniae"
by Kloosterman et al.

first: Tomas

last: Kloosterman

first: Robert

last: Witwicki

first: Magdalena

last: Pol

first: Jetta

middle: J

last: Bijlsma

first: Oscar

middle: P

last: Kuipers


title: Expression data from chicken adipose tissue at 7-week of age

city: Harbin

first: Hongbao

last: Wang

address: No. 59 Mucai Street, Xiangfang District

institute: Northeast Agricultural University

summary:
Excessive accumulation of lipids in the adipose tissue is a major problem in the present-day broiler industry. However, few studies have analyzed the expression of adipose tissue genes that are involved in pathways and mechanisms leading to adiposity in chickens. Gene expression profiling of chicken adipose tissue could provide key information about the ontogenesis of fatness and clarify the molecular mechanisms underlying obesity.
Chicken Genome Arrays were used to construct an adipose tissue gene expression profile of 7-week-old broilers, and to screen adipose tissue genes that are differentially expressed in lean and fat lines divergently selected over eight generations for high and low abdominal fat weight.
Keywords: two lines comparison

overall_design: Birds were slaughtered at 7 weeks and abdominal fat was isolated, immediately frozen in liquid nitrogen and stored at -80oC. The ten birds used in the present study were chosen by the percentage of abdominal fat (AFP): five had the highest AFP and the other five had the lowest for RNA extraction and hybridization on Affymetrix microarrays..

first: Hui

last: Li

first: Qigui


title: Global transcriptional activity in pluripotent embryonic stem cells.

status: Public on May 14 2008

city: Santa Clara

first: Thomas

middle: R

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

summary:
The molecular mechanisms underlying pluripotency and lineage specification from embryonic (ES) cells are largely unclear. Differentiation pathways may be determined by the targeted activation of lineage specific genes or by selective silencing of genome regions during differentiation. Here we show that large fractions of the ES cell genome are transcriptionally active and undergo global silencing as cells differentiate. Normally silent repeat regions are active in ES cells and tissue-specific genes are sporadically expressed at low levels. Whole genome tiling arrays demonstrate widespread transcription in both coding and non-coding regions in pluripotent ES cells whereas the transcriptional landscape becomes more discrete as differentiation proceeds. The transcriptional hyperactivity in ES cells is accompanied by disproportionate expression of chromatin-remodeling and the general transcription machinery, but not histone modifying activities. Interference with several chromatin remodeling activities in ES cells affects their proliferation and differentiation behavior. We propose that global transcriptional activity is a hallmark of pluripotent ES cells that contributes to their plasticity and that lineage specification is strongly driven by reduction of the actively transcribed portion of the genome.
Keywords: mouse embryonic stem cell, time course profiling, tiling array,  transcriptome

overall_design: A total of 4 samples from a differentiation time course of mouse embryonic stem cell(i.e 00hr ES state, 12 hr EB state, 24 hr EB state and 168hr NPC state) were analyzed. Three independent biological replicas were generatedfor each of these samples and hybridized to the Mouse Tiling 1.0R array containing the entire mouse non-repetitive genome in 16 chips at 30bp resolution as measured from the central position of adjacent 25-mer oligonucleotides. Taken together hybridization data from 192 chips were collected to generate whole genome transcriptome information for this study.

first: S

last: Efroni

first: R

last: Duttagupta

first: J

last: Cheng

first: H

last: Dehghani

first: D

last: Hoeppne

first: C

last: Dash

last: Bazett-Jones

middle: L

last: Grice

last: McKay

first: K

middle: H

last: Buetow

first: T

last: Misteli

first: E

last: Meshorer


title: Age-related changes in the expression of schizophrenia susceptibility genes in the human prefrontal cortex

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

summary:
The molecular basis of complex neuropsychiatric disorders most likely involves many genes. In recent years, specific genetic variations influencing risk for schizophrenia and other neuropsychiatric disorders have been reported. We have used custom DNA microarrays and qPCR to investigate the expression of putative schizophrenia susceptibility genes and related genes of interest in the normal human brain. Expression of 31 genes was measured in Brodmann's area 10 (BA10) in the prefrontal cortex of 72 postmortem brain samples spanning half a century of human aging (18-67 years), each without history of neuropsychiatric illness, neurological disease, or drug abuse. Examination of expression across age allowed the identification of genes whose expression patterns correlate with age, as well as genes that share common expression patterns and that possibly participate in common cellular mechanisms related to the emergence of schizophrenia in early adult life. The expression of GRM3 and RGS4 decreased across the entire age range surveyed, while that of PRODH and DARPP-32 was shown to increase with age. NRG1, ERBB3, and NGFR show expression changes during the years of greatest risk for the development of schizophrenia. Expression of FEZ1, GAD1, and RGS4 showed especially high correlation with one another, in addition to the strongest mean levels of absolute correlation with all other genes studied here.

Keywords: postmortem human brain collection

Supplementary files:
Gene expression measures in Matrix1379Normalized.txt include all data from the 1379 probes on the arrays, and are NOT adjusted for PMI, brain pH, and RIN, and are NOT averaged over multiple probes within genes.
Raw data are located in Raw_1241842_gene_probe_profile.txt.

overall_design: We have used custom DNA microarrays to investigate gene expression in the normal human brain. Expression was measured in Brodmann's area 10 (BA10) in the prefrontal cortex of 72 postmortem brain samples spanning half a century of human aging (18-67 years), each without history of neuropsychiatric illness, neurological disease, or drug abuse.

last: Hyde

first: Shruti

last: Mitkus

first: Andrew

last: Joseph

first: Leah

last: Sartorius

first: Claudia

last: Aguirre

first: Johanna

last: Creswell

first: Elizabeth

last: Johnson

first: Amy

last: Deep-Soboslay

first: Mary

last: Herman

first: Barbara

middle: K

last: Lipska

first: Daniel

last: Weinberger

first: Joel

middle: E

last: Kleinman


title: Transcript Profiling of High Fat Diet induced Obesity-prone and Obesity-resistant Rats

city: shanghai

first: Zhang

last: Qinghua

address: 151# libing road

institute: Shanghai shbiochip co

summary: Rodents respond to chronic high fat diet in at least two ways: some of them may readily gain body weight and become obese (termed obesity-prone), and others may not (termed obesity-resistant).  An integrated approach of transcript and metabolic profiling of obesity-prone and obesity-resistant rats has been conducted, showing significantly different transcript and metabolic profiles in the two phenotypes.  The major transcriptional differences involved hepatic fatty acid metabolism and ketogenesis in response to 16 weeks of high fat diet.  At the same time, the different metabolic profiles (in liver tissue extracts, serum, and urine) between the two phenotypes could be ascribed to the corresponding pathways identified with multivariate statistical analysis, including fatty acid metabolism, Krebs cycle, and amino acid metabolism.  The integration of results from both transcript and metabolic profiling revealed the different responses to dietary intervention of the two phenotypes and the physiological basis of susceptibility to metabolic disease in obesity-prone rats from a systematic view.

overall_design:
We developed OP and OR phenotypes in a group of Wistar rats by maintaining them on a HFD for 16 weeks, and subsequently analyzed their hepatic transcript profile using cDNA microarrays, the rats were feed on standard chow diet for 16 weeks as control. Four rats were selected for transcript analysis in each group.
The four control rats were mixed and labeled with cy5, each OP or OR rats were labeled with cy3.

Label protocol: 2 ug of total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65 ℃ for 10 min, then reversed transcribed at 40℃ for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent). cDNAs were amplified at 40℃for 2 hours in the presence of T7 RNA Polymerase (Agilent) and 4 ul 25mM aaUTP (Ambion).Generated cRNA was purified with RNeasy mini Kit (QIAGEN).Mix 4 ug amino allyl-modified cRNA and 100mg Cy3 NHS ester, incubate in the dark at room temperature (~25 ℃) for 1 hour then purified with RNeasy mini Kit (QIAGEN).

Hybridization protocol: After mixed with hybridization buffer (GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box.Incubate in a hybridization chamber at 42 ℃ for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1×SSC/0.2 SDS(50℃), 0.1×SSC/0.2%SDS(50 ℃) and 0.1×SSC(room temperature) before scanning.

Scan protocol: Axon GenePix 4000B

Description: Total RNA was prepared from rat livers using Trizol reagent (Invitrogen, USA), and further purified with an QIAGEN RNeasy Kit. Then, 2 ug of total RNA were amplified using Low RNA Input Linear Amplification Kit (Agilent, USA), and labeled with amino allyl-modified cRNA labeling kit (Ambion, USA). Equal amounts of the RNA from four control rats were mixed, and the mixture was labeled with Cy5, while the RNA from OP and OR rats was labeled with Cy3. The Cy5 and Cy3 probes were mixed and hybridized at 42 ℃ for 16 h. The two fluorescent images (Cy3 and Cy5) were scanned separately by Agilent Scanner G2565BA, and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

Data processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Green signal/processed Red signal (high fat diet rat/control rat).

first: Houkai

last: Li

first: Zuoquan

last: Xie

first: Qi

last: Wang

first: Zhidong

last: Zhu

first: Qinghua

last: Zhang

first: Wei

last: Jia


title: Comparison among longissimus dorsi muscle of 3 pig breeds, among developmental phases of Tibetan Pig

status: Public on May 15 2008

city: Ya'an

first: Mingzhou

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary:
The objective of this study was to identify key genes associated with porcine muscle growth and adipose metabolism which different expression in porcine longissimus dorsi muscle tissue among Tibetan Pig, Taihu Pig and Landrace(Month 2), among developmental phases of Tibetan Pig (Month 2,4,6,8). The gene expression analyses will increase understanding of impact factors of pork quality by identifying key genes and pathways controlling longissimus dorsi muscle development. Relative real-time RT-PCR was used to confirm differential expression of 5 different expression genes(PPARGC1A, RYR1, IGF2, IGF1R and IGFBP5) which normalized by 3 housekeep genes(ACTB, TBP and TOP2B).
Keywords: breed comparison and time course

overall_design:
The different expression experiments among Tibetan Pig, Taihu Pig and Landrace used  indirect loop design(Month2:Tibetan Pig vs Landrace, Landrace vs Taihu Pig ,Taihu Pig vs Tibetan Pig).
The different expression experiments among developmental phases of Tibetan Pig (Month 2,4,6,8) used direct-sequential design (Tibetan Pig:Month 4 vs Month 2, 6 vs 4,8 vs 6).

first: Xuewei

first: Li

first: Yujiao

last: Guo

first: Lei

last: Chen

first: Qiang

first: Surong

last: Shuai

first: Anan

last: Jiang

first: Guangxi

last: Yang

first: Guoqing

last: Tang

first: Yanzhi


title: Genomic expression patterns of mitral valve tissues from dogs with degenerative mitral valve disease

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
Evaluation of global expression patterns provides a molecular portrait of mitral valve disease, yields insight into the pathophysiologic aspects of DMVD, and identifies intriguing genes and pathways for further study. (Am J Vet Res 2006;67:1307–1318)
Keywords: control vs diseased

overall_design: 4 controls( beagle crosses) and 4 affected (1 Daschund, 1 Lhasa apso, 2 miniature poodles)

first: Mark

last: Oyama


title: Adult Human Chondrocyte Response to IL-1B

city: St. Louis

first: Debabrata

last: Patra

state: MO

address: 425 S. Euclid Avenue

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary:
IL-1B is an important cytokine that is often found to be up-regulated during osteoarthritic and rheumatoid joint diseases.  It is viewed as a catabolic factor, inducing enzymes that allow for the degradation of the cartilage extracellular matrix and also has essential roles as an autocrine and paracrine factor in fibronectin fragment-mediated degradation.  It can also reduce the synthesis of the major cartilage components, type II collagen and aggrecan.  On the other hand, IL-1B also has the ability to induce the growth and morphogenic factor BMP-2.  During joint diseases, IL-1B is synthesized by both synovial cells and chondrocytes.  Addition of IL-1 biological antagonists such as IL-1 receptor antagonists can suppress cartilage degradation in vitro.  Thus, the production of IL-1B could act as the first step in mediating a cascade of other mediators in cartilage which could be relevant to the fate of the cartilage.  In order to obtain a global picture of the effect of IL-1B production on human adult articular chondrocytes, we analyzed changes in gene expression induced by IL-1B by microarray analysis.  We found that IL-1B has a diverse effect on gene expression profile in chondrocytes.  One of the predominant responses that we observed in adult human articular chondrocytes on exposure to IL-1B is a dramatic increase in a large set of chemokines and other genes related to the inflammatory cascade.
Keywords: Gene response to IL-1B (10 ng/ml)

overall_design: Cartilage was obtained from adult human tissue donors with above the knee amputations due to chondrosarcoma or traumatic injury or from autopsy.  Chondrocytes were isolated following established protocols, maintained in high density, and treated with IL-1B (10 ng/ml).  Chondrocytes treated with buffer only served as the untreated control.  The experiment was carried out in duplicate.  Total RNA was extracted from these chondrocytes, labeled with fluorophores (Cy3 or Cy5) and analyzed for expression changes using the Human Operon/Qiagen v3.0 oligonucleotide array.  The analysis was repeated with the fluorophore dyes exchanged between the untreated and experimental RNAs.

first: Linda

last: Sandell

first: Xiaoyun

last: Xing

first: Carl

last: Franz

first: Sherri

last: Davies

first: Li-Wei

last: Chang


title: Radiation-Induced Changes in Gene Expression Involve Recruitment of Existing Messenger RNAs to and from Polysomes

city: Gaithersburg

first: Shuping

last: Zhao

address: 8717 Grovemont Circle

department: Radiation Oncology Branch

institute: NCI

summary: Although ionizing radiation has been shown to influence gene transcription, little is known about the effects of radiation on gene translational efficiency. To obtain a genome-wide perspective of the effects of radiation on gene translation, microarray analysis was done on polysome-bound RNA isolated from irradiated human brain tumor cells; to allow for a comparison with the effects of radiation on transcription, microarray analysis was also done using total RNA. The number of genes whose translational activity was modified by radiation was f10-fold greater than those whose transcription was affected. The radiation-induced change in a gene’s translational activity was shown to involve the recruitment of existing mRNAs to and away from polysomes. Moreover, the change in a gene’s translational activity after irradiation correlated with changes in the level of its corresponding protein. These data suggest that radiation modifies gene expression primarily at the level of translation. In contrast to transcriptional changes, there was considerable overlap in the genes affected at the translational level among brain tumor cell lines and normal astrocytes. Thus, the radiation-induced translational control of a subset of mRNAs seems to be a fundamental component of cellular radioresponse. (Cancer Res 2006; 66(2): 1052-61)

overall_design:
There are 32 samples in total in this study. Each sample has a technical duplicate (16samples x2). Comparison of radiation-induced gene expression profiles generated from microarray analysis of total and polysome-bound RNA isolated from three brain tumor cell lines U87, SF126, SF539 and normal astrocytes. Cells were irradiated at the dose of 7gy and collected 6 hours later for isolation of total cellar RNA or polysome-bound RNA. Gene expression was directly compared between irradiated and unirradiated control cells for total and polysome RNA.

The array labeling is two-dye method. Labeling two dye samples are labeled using CY3 dye. All the human reference RNA from Stratagene are labeled using CY5 dye.

first: Xing

last: Lv

first: Lorena

last: Pena

first: Christopher

last: Barker

first: Kevin

last: Camphausen

first: Philip

last: Tofilon