Double-tiled DNA microarrays -- proof of principle
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE5721 | GEO | 2006/10/23
SECONDARY ACCESSION(S): PRJNA97017
REPOSITORIES: GEO
Similar Datasets
Project description:In this work we demonstrate a novel method of methylation detection that utilises immunoaffinity to detect the presence of methylated DNA hybridised to a cDNA microarray. We use a monoclonal antibody specific to 5 methylcytosine to detect the presence of 5 methylcytosine in genomic DNA from human fibroblasts bearing the karyotype 45 XO. We report that over 2900 genes show the presence of methylation in this condition. We also report that 165 genes are consistently methylated in all replicates of these experiments. The methylated genes show a uniform distribution over all the chromosomes. The gene ontology of these also indicates no functional correlation between the genes that are methylated. We detect the presence of methylation in IGF2, an imprinted gene and thus known to harbour DNA methylation. The method is extremely specific and offers a quick and efficient way to analyse the methylation landscape on a high throughput scale. This method uses existing technology to assess methylation and thus can integrate very efficiently into any platform used. A method that detects DNA methylation that is not restricted to specific sequences would provide a useful platform to analyse methylation distribution among the genes in any given phenotypic condition.Availability of additional approaches to examine DNA methylation would lead to increase in our understanding of the methylome and would help define the intrinsic and extrinsic factors which govern it. Microarray based high throughput methods have been extensively used for gene expression analysis. The method described uses a microarray to analyse DNA methylation levels in a gene/cDNA/oligo specific manner. Here, genomic DNA is fragmented and used for hybridization to microarray slides. The presence of DNA cytosine methylation in the hybridized DNA is detected by employing Cy3 labelled anti 5mC( 5-methyl cytidine) antibody (monoclonal). The resolution provided by this method is dependent upon the microarray platform used. This method can be adapted to any platform thus enabling seamless integration with existing technology of gene expression analysis
2010-04-09 | GSE20873 | GEO
Project description:The complete genome sequence of the P. vivax Sal-1 strain allowed the design of a first version array representing 1 oligo/2 kb of coding sequences (http://zblab.sbs.ntu.edu.sg/vivax/index.html). Here, proof-of-principle experiments using total RNA of parasites obtained from the Sal-1 strain, from P. falciparum and from parasites obtained directly from two human patients are presented. Keywords: expression profiles
2008-04-12 | GSE11075 | GEO
Project description:The complete genome sequence of the P. vivax Sal-1 strain allowed the design of a first version array representing 1 oligo/2 kb of coding sequences (http://zblab.sbs.ntu.edu.sg/vivax/index.html). Here, proof-of-principle experiments using total RNA of parasites obtained from the Sal-1 strain, from P. falciparum and from parasites obtained directly from two human patients are presented. To determine the extent of cross-hybridization of P. falciparum with P. vivax, and to determine overlaps in expression profiles of the P. vivax Sal1 monkey-adapted strain vs wild isolates, single dual hybridization analyses were performed.
2008-04-12 | E-GEOD-11075 | biostudies-arrayexpress
Project description:We have developed a multi-analyte fluid-phase protein array technology termed high-throughput immunophenotyping using transcription (HIT). This method employs a panel of monoclonal antibodies, each tagged with a unique oligonucleotide sequence that serves as a molecular barcode. After staining a sample, T7 polymerase amplifies the tags which are then hybridized to a DNA microarray for indirect measurement of each analyte. Here we coupled 44 of the tags to aliquots of an IgG1 isotype negative control antibody and the 4 remaining tags we coupled to anti-CD3, anti-CD4, anti-CD19, and anti-CD20 to create a 48-plex HIT cocktail. We then used this cocktail to stain 1 x 10^6 T or B cells and during amplification incorporated either cyanine 3-UTP (Cy3-UTP) or Cy5-UTP. Additionally, we snap froze and thawed an aliquot of the cocktail (FT). Keywords: protein profiling, cell type comparison Two-condition experiment, T cells versus B cells, including dye-swaps and self-self experiments. We also tested an array that had been frozen and thawed.
2010-05-26 | E-GEOD-10761 | biostudies-arrayexpress
Project description:We have developed a multi-analyte fluid-phase protein array technology termed high-throughput immunophenotyping using transcription (HIT). This method employs a panel of monoclonal antibodies, each tagged with a unique oligonucleotide sequence that serves as a molecular barcode. After staining a sample, T7 polymerase amplifies the tags which are then hybridized to a DNA microarray for indirect measurement of each analyte. Here we coupled 44 of the tags to aliquots of an IgG1 isotype negative control antibody and the 4 remaining tags we coupled to anti-CD3, anti-CD4, anti-CD19, and anti-CD20 to create a 48-plex HIT cocktail. We then used this cocktail to stain 1 x 10^6 T or B cells and during amplification incorporated either cyanine 3-UTP (Cy3-UTP) or Cy5-UTP. Additionally, we snap froze and thawed an aliquot of the cocktail (FT). Keywords: protein profiling, cell type comparison
2008-03-08 | GSE10761 | GEO
Project description:Liquid biopsy profile which can screen for early CRC. We aimed to depict the profile of early stage CRC as well as for advanced adenomas by combination of current molecular knowledge with microarray technology, using efficient circulating free RNA purification from blood and RNA amplification technologies. Circulating free RNA profile of plasma from colorectal cancer patients, advanced adenomas and healthy colonoscopia subjects.
2016-06-15 | GSE83353 | GEO
Project description:Liquid biopsy profile which can screen for early CRC. We aimed to depict the profile of early stage CRC as well as for advanced adenomas by combination of current molecular knowledge with microarray technology, using efficient circulating free RNA purification from blood and RNA amplification technologies. Circulating free RNA profile of plasma from colorectal cancer patients, advanced adenomas and healthy colonoscopia subjects. Plasma was drawn from 3 healthy colonoscopia subjects, 4 adanced adenomas subjects and 3 colorectal cancer patients. Circulating free RNA was purified from plasma samples and applied on GeneChip human 1.0 ST Arrays. The 'HuGene_1_0_green_yelow_red_DATASET.xlsx' and 'probe_level_expression_matrix.txt' files contain the primary data that was used to draw the conclusions of the current study. Please note that exon-level' analysis was performed but NO probe summarization to probeset was performed, therefore both data matrices contains non-unique identifiers.
2016-06-15 | E-GEOD-83353 | biostudies-arrayexpress
Project description:Long non-coding ribonucleic acids (lncRNAs) have been proposed as biomarkers in prostate cancer. This paper proposes a selection method which uses data from tiled microarrays to identify relatively long regions of moderate expression independent of the microarray platform and probe design. The method is used to search for candidate long non-coding ribonucleic acids (lncRNAs) at locus 8q24 and is run on three independent experiments which all use samples from prostate cancer patients. The robustness of the method is tested by utilizing repeated copies of tiled probes. The method shows high consistency between experiments that used the same samples, but different probe layout. There also is statistically significant consistency when comparing experiments with different samples. The method selected the long non-coding ribonucleic acid PCNCR1 in all three experiments.
| S-EPMC4061049 | biostudies-literature
Project description:Picky is an optimal microarray design software which designed the NSF Rice 45K Array. A series of microarray experiments using a one-chip version of this array were conducted to validate as well as to develop a calibration method for Picky designed microarrays. Synthesized samples with known content were used in the validation. PICKY designed microarrays were found to be highly reliable. The PICKY predicted closest nontarget information was used to quantitatively calibrate the best microarray hybridization conditions using the same microarrays and synthesized samples. Because this method works under most microarray protocols, it is generally applicable in any lab that uses PICKY as their microarray design tool. The associate publication provides more details about the experiment design and discussions about its results. Keywords: Microarray Calibration
2009-10-22 | GSE14717 | GEO
Project description:Mapping DNase I hypersensitive sites is an accurate method of identifying the location of gene regulatory elements, including promoters, enhancers, silencers and locus control regions. Although Southern blots are the traditional method of identifying DNase I hypersensitive sites, the conventional manual method is not readily scalable to studying large chromosomal regions, much less the entire genome. Here we describe DNase-chip, an approach that can rapidly identify DNase I hypersensitive sites for any region of interest, or potentially for the entire genome, by using tiled microarrays. We used DNase-chip to identify DNase I hypersensitive sites accurately from a representative 1% of the human genome in both primary and immortalized cell types. We found that although most DNase I hypersensitive sites were present in both cell types studied, some of them were cell-type specific. This method can be applied globally or in a targeted fashion to any tissue from any species with a sequenced genome.
| S-EPMC2698431 | biostudies-literature