Transcriptome analysis of mononuclear cells derived from bone marrow of pediatric patients with acute myeloid leucosis, acute lymphoid leucosis and from heathy donors peripheral blood
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Maria Suntsova
PROVIDER: E-GEOD-84575 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The aim of this research was to explore activation/deactivation of signaling pathways in mononuclear cells from pediatric patients with acute myeloid leucosis and acute lymphoid leucosis. Mononuclear cells were separated shortly after bone marrow samples collection. Cells were obtained by a density gradient centrifugation method using Ficoll. Cells were dissolved in RNALater solution, aliquoted and stored at -20°C till RNA extraction and microarray hybridisation.
2016-07-20 | E-GEOD-84574 | biostudies-arrayexpress
Project description:Orientia tsutsugamushi, an obligate intracellular bacterium, is the causative agent of Scrub typhus. The bacterium can replicate both in its arthropod host and in mammals, including humans. The control mechanisms for bacterial gene expression within eukaryotic host cells are largely unknown. Previously, we reported that the O. tsutsugamushi genome has the highest repeat density of any sequenced bacterial genome due to the extraordinary proliferation of mobile genetic elements (MGEs), suggesting a unique genomic evolution in intracellular niches. In this study, the global gene expression of O. tsutsugamushi within eukaryotic cells was examined using a microarray and proteomic approaches. These approaches identified 643 genes, corresponding to approximately 30% of genes encoded in the genome. The majority of expressed genes belonged to several functional categories including protein translation, protein processing/secretion, and replication/repair. We also searched the conserved sequence blocks (CSBs) in the genomes of different O. tsutsugamushi strains to identify gene blocks impermeable to proliferating MGEs. Although extensive shuffling of genomic sequences was observed between two different strains, 204 CSBs with sizes ranging from 1 kbp to 29 kbp, covering 48% of the genome, were identified. When combining the data of the CSBs and global gene expression, CSBs in the O. tsutsugamushi genomes correlates well with the location of expressed genes, especially in protein level, suggesting the functional conservation between gene expression and genomic location. Finally, we compared global gene expression of the bacteria infecting fibroblasts and macrophages using microarray analysis. Major changes in the expression of genes with known functions were the downregulation of genes involved in translation, protein processing and secretion, which resulted in significant reduction in bacterial translation rates and growth within macrophages. These results suggest that the replication of O. tsutsgamushi is controlled primarily by the expression of genes involved in bacterial translation and subsequent protein processing/secretion. Microarray analysis using the Combimatrix CustomArrayTM 4X2 microarray (CombiMatrix) was performed according to the standard CombiMatrix protocol described in detail at http://www.combimatrix.com/ products_custom4x2.htm (PTL005). Oligonucleotide probes (27 to 40-mers, 1613 probes) were designed for 1472 CDSs of the O. tsutsugamushi genome (GeneBank accession no. AM494475). 1 to 6 probes per CDS were designed and some probes were duplicated on the microarray (total 2187 spots on an array). As negative controls, 5 and 15 oligonucleotide probes derived from plant and bacteriophage respectively were spotted on the array at 53 sites per array. A local background subtraction method was used and the background-subtracted signal values were imported into the Avadis Prophetic software (ver. 3.3, Strand Genomics) or Expander (ver. 4.1, http://acgt.cs.tau.ac.il/expander/) for data analysis. . Global normalization of gene expression data was performed using the quantile normalization method embedded in the Expander software. The standard deviations of log data and the p-values were calculated using default settings in the Avadis software. Transcriptome analysis was carried out using three biological replicates for uninfected samples (uninfected L929 cells) and five biological replicates for infected samples (L929 cells infected with O. tsutsugamushi for 48 h). For comparison of the O. tsutsugamushi transcriptome from fibroblasts (L929 cells) and macrophages (J774A.1 cells), two biological replicates from each cell line were used.
2010-06-05 | E-GEOD-16966 | biostudies-arrayexpress
Project description:Individualized outcome prediction classifiers were successfully constructed through expression profiling of 1918 genes connected with lipid metabolism in yeast strain overexpressed of fatty acid biosynthesis gene In the study presented here, expression profiles of wild type and ACC-overexpressed wild type yeast strain were well-clustered by profiles- and gene similarities. It was analyzed the gene expression profile of ACC-overexpressing as compared with those of wild type. The expression levels between wild type(WT) and ACC-overexpressed wild type(ACC) were compared individually three times.
2012-01-13 | E-GEOD-35041 | biostudies-arrayexpress
Project description:The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including mobile genetic elements (MGE) encoding antimicrobial resistance. Here, we define the mobilome in representative successful hospital associated genetic lineages, E. faecium ST17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) using DNA microarray analyses. The hybridization patterns of 272 targets representing plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29), and CRISPR-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. Although plasmids belonging to the RCR-, Rep_3-, RepA_N- and Inc18-families were well represented with no significant differences in prevalence, the presence of specific replicon classes differed highly between the species; E. faecium was dominated by rep17/pRUM, rep2/pRE25, rep14/EFNP1 and rep20/pLG1 and E. faecalis by rep9/pCF10, rep2/pRE25 and rep7. Tn916-elements conferring tetracycline resistance (tetM) were found in all E. faecalis strains, but only in two E. faecium strains. A significant higher prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982-, and IS4-transposases were detected in E. faecium, and of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 which have only been reported in few enterococcal isolates, were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented. Gene targets defined as the enterococcal mobilome, including plasmids, IS elements and transposons, resistance determinants, prophage sequences and CRISPR-Cas systems were highly prevalent, underlining their potential importance in the evolution of hospital associated STs. An association between axe-txe to the RepA_N-family and M-OM-^I-M-NM-5-M-NM-6 to the Inc18-family, implicates the contribution of TA-systems in stable plasmid maintenance carrying virulence and resistance determinants in enterococci. The concurrent presence of defined MGE and their associated resistance markers was generally confirmed and illustrates the importance of horizontal gene transfer in the development of multidrug resistant enterococci. All together 272 DNA targets representing mobile genetic elements and antimicrobial resistance determinants associated with enterococci were spotted on a CustomArray 4x2K microarray from CustomArray Inc. Each fourplex microarray slide contain four identical sectors that were stripped and re-hybridized up to six times. Each target was represented by 1-5 probes each. The total of 1250 probes were Tm balanced by altering their lenght between 35 and 40 nucleotides. Total DNA of 41 samples were hybridized and a control strain, the fully sequenced E. faecalis V585, was included in one of the four sectors on each slide in each set of hybridization to monitor the overall array and hybridization quality.
2014-07-08 | E-GEOD-59190 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are a highly conserved class of small RNAs which function in a sequence-specific manner to post-transcriptionally regulate expression of target genes. Tissue-specific miRNA expression studies have discovered numerous functions for miRNAs in various aspects of embryonic development, but a role for miRNAs in gonadal development and sex differentiation has not yet been reported. Using the chicken embryo as a vertebrate model, differential miRNA expression between male and female embryonic gonads, was analysed at three developmental stages (embryonic days (E) 5.5, E6.5 and E9.5), using custom-designed 4x2K CombiMatrix miRNA microarray. The aims of this study were to: 1-identify miRNAs differentialy expressed by sex; 2-identify sex-specific miRNAs; 3-analyse global changes in miRNA up-regulation in male versus female gonads before, during and after the histological onset of sexual differentiation. This study provides a basis for establishing whetehr miRNAs are involved in either initiating or regulating vertebrate gonadal sex differentiation. Keywords: miRNA, sex comparison, developmental stage comparison. miRNA samples from male and female embryonic chicken gonads from three developmental stages: embryonic day (E) 5.5 (Hamilton & Hamburger (HH) stage 27-28), E6.5 (HH stage 29-30) & E9.5 (HH stage 35-36). Samples are listed with biological replicates used for analysis in brackets following: 1 - Male E5.5 (5); 2 - Female E5.5 (4); 3 - Male E6.5 (5); 4 - Female E6.5 (3); 5 - Male E9.5 (4); 6 - Female E9.5 (4).
2010-05-18 | E-GEOD-13154 | biostudies-arrayexpress
Project description:The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation:DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e., concentration in seawater) and in a relative sense (i.e., proportionally to other labile organic S compounds) being proposed as the critical factor. We investigated these models during an experimentally-induced phytoplankton bloom using an environmental microarray targeting DMSP-related gene expression in the Roseobacter group, a taxon of marine bacteria known to play an important role in the surface ocean sulfur cycle. The array consisted of 1,578 probes to 431 genes, including those previously linked to DMSP degradation as well as core genes common in sequenced Roseobacter genomes. The prevailing pattern of Roseobacter gene expression showed depletion of DMSP-related transcripts during the peak of the bloom, despite the fact that absolute concentrations and flux of DMSP-related compounds were increasing. A likely interpretation is that DMSPd was assimilated by Roseobacter populations in proportion to its relative abundance in the organic matter pool (the “relative sense” hypothesis), and that it is not taken up in preference to other sources of labile organic sulfur or carbon produced during the bloom. The relative investment of the Roseobacter community in DMSP demethylation did not predict the fractional conversion of DMSP to DMS, however, suggesting a complex regulatory process that may involve multiple fates of DMSPd. DMSP-related gene expression in the Roseobacter group was investigated using an environmental microarray. Coastal seawater from the Gulf of Mexico was collected and dispensed into 20-L microcosms. Two replicate cubitainers were amended with nutrients (N and P) to stimulate phytoplankton bloom, while two untreated cubitainers served as controls. The microcosms were incubated at 27ºC in a temperature-controlled incubator on a 12 h light/dark cycle for total of 7 days. Ten RNA samples (Day 0: 2 conditions with 1 biological replicate each; Days 2 and 4: 2 conditions with 2 biological replicates each) were prepared for microarray hybridization. After total RNA extraction, rRNAs were removed and mRNA transcripts were amplified and labeled with Alexa Fluor 647. Two technical replicates were hybridized from each RNA sample. The microarray was designed based on selected Ruegeria pomeroyi DSS-3 genes and their orthologs in 12 other sequenced Roseobacter genomes. Probes were designed from the orthologs using the Hierarchical Probe Design (HPD) algorithm.
2010-08-05 | E-GEOD-21325 | biostudies-arrayexpress
Project description:Grape berries undergo considerable physical and biochemical changes during the ripening process. Ripening is characterized by a number of changes, including the degradation of chlorophyll, an increase in berry deformability, a rapid increase in the level of hexoses in the berry vacuole, an increase in berry volume, the catabolism of organic acids, the development of skin colour, and the formation of compounds that influence flavour, aroma, and therefore, wine quality. The aim of this work is to identify differentially expressed genes during grape ripening by microarray and real-time PCR techniques. Using a custom array of new generation, we analysed the expression of 6000 grape genes from pre-veraison to full maturity, in Vitis vinifera cultivar Muscat of Hamburg, in two different years (2006 and 2007). Five time points per year and two biological replicates per stadium were considered. To reduced intra-plant and inter-plant biological variability, for each ripening stadium we collected around hundred berries from several bunch grapes of five plants of V. vinifera cv Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.
2010-11-09 | E-MEXP-2451 | biostudies-arrayexpress
Project description:Acute myeloid leukemia (AML) is the most common and severe acute leukemia diagnosed in adults. Although it is one of the most studied cancers, this is the first study of Polish population of AML patients. The data were collected with the use of home-made boutique array. The additional advantage is pre-selection of patients - our sample set includes only two AML FAB subtypes with the highest content of immature myeloid cells: M1 (11 samples) and M2 (22 samples). From the majority of patients two sources of material were used for mononuclear cell separation and RNA extraction: bone marrow and peripheral blood. 15 samples from healthy volunteers were used as a control.
2017-12-31 | E-MTAB-5434 | biostudies-arrayexpress
Project description:In this study we analyzed the effects of CRY2 over-expression on chloroplast genome transcription of tomato, by developing and using a tiling array. This array containing about 90,000 overlapping probes (5-nt resolution) is a versatile tool for global functional studies of tomato cp genome. We profiled transcription in leaves of wild-type (WT) and CRY2-overexpressing (CRY2-OX) plants grown in a diurnal cycle, to generate a comprehensive map of plastid transcription and to monitor potential specific modulations of chloroplast transcriptome induced by the overexpression of CRY2.
2016-06-24 | E-MTAB-1757 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE33387: NanoString miRNA profiling of peripheral blood mononuclear cells from HIV-1-infected elite suppressors, viremic patients, and uninfected control donors GSE33492: TaqMan Peripheral blood mononuclear cell miRNA profiles of HIV-1-infected elite suppressors, viremic patients, and uninfected control donors Refer to individual Series
2012-02-22 | E-GEOD-33617 | biostudies-arrayexpress