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*  Comparative genomic hybridization
... array CGH is also suitable for the analysis of DNA copy number aberrations that cause human genetic disorders. That is, array ... The latest approach is spotting the arrays with short oligonucleotides. The amount of oligos is almost infinite, and the ... makes it possible to map the changes directly onto the genomic sequence. Array CGH has proven to be a specific, sensitive, fast ... Arrays can also be constructed using cDNA. These arrays currently yield a high spatial resolution, but the number of cDNAs is ...
*  Gene expression profiling in cancer
Techniques include DNA microarray technology or sequenced-based techniques such as serial analysis of gene expression (SAGE). ... makes use primarily of DNA microarrays in which an arrayed series of microscopic spots of pre-defined DNA oligonucleotides ... Survival analyses are often shown as Kaplan-Meier survival plots, an example of which is shown to the right. In addition to ... DNA microarrays evolved from Southern blotting which allows for detection of a specific DNA sequence in a sample of DNA. Due to ...
*  Gene expression profiling
2007). "A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in ... Therefore, gene set analysis is considered a knowledge based analysis approach. Commonly used gene sets include those derived ... "A comparison of statistical tests for detecting differential expression using Affymetrix oligonucleotide microarrays". OMICS. ... Sequence based techniques, like RNA-Seq, provide information on the sequences of genes in addition to their expression level. ...
*  List of MeSH codes (E05)
... oligonucleotide array sequence analysis MeSH E05.393.760.640 --- oligonucleotide array sequence analysis MeSH E05.393.760.700 ... oligonucleotide array sequence analysis MeSH E05.588.570.700 --- protein array analysis MeSH E05.588.570.850 --- tissue array ... oligonucleotide array sequence analysis MeSH E05.196.630.570.700 --- protein array analysis MeSH E05.196.630.570.850 --- tissue ... oligonucleotide array sequence analysis MeSH E05.393.525.680 --- protein array analysis MeSH E05.393.525.700 --- random ...
*  DNA microarray
"Light-generated oligonucleotide arrays for rapid DNA sequence analysis". PNAS. 91 (11): 5022-5026. doi:10.1073/pnas.91.11.5022 ... Oligonucleotide arrays are produced by printing short oligonucleotide sequences designed to represent a single gene or family ... In oligonucleotide microarrays, the probes are short sequences designed to match parts of the sequence of known or predicted ... Although oligonucleotide probes are often used in "spotted" microarrays, the term "oligonucleotide array" most often refers to ...
*  Biochip
"Light-generated oligonucleotide arrays for rapid DNA sequence analysis," Proc. Natl. Acad. Sci. 91, pp. 5022-5026, 1994 F. J. ... launched Evidence, the first protein Biochip Array Technology analyzer in 2003. In protein Biochip Array Technology, the ... "Fluorescence detection in automated DNA sequence analysis," Nature 321, pp. 61-67, 1986 P. Fortina, D. Graves, C. Stoeckert, Jr ... These arrays must be made using a serial process (i.e. requiring multiple, sequential steps) to ensure that each sensor is ...
*  Oligonucleotide synthesis
"Light-generated oligonucleotide arrays for rapid DNA sequence analysis". Proc. Natl. Acad. Sci. U.S.A. 91 (11): 5022-5026. ... one oligonucleotide sequence occupies a square 25×25 μm) and the requirement of high fidelity of oligonucleotide synthesis ... They are most commonly used as antisense oligonucleotides, small interfering RNA, primers for DNA sequencing and amplification ... Willems, A.; Deforce, D. L.; Van Bocxlaer, J. (2008). Analysis of oligonucleotides using capillary zone electrophoresis and ...
*  Bayesian tool for methylation analysis
It can be applied to large datasets generated using either oligonucleotide arrays (MeDIP-chip) or next-generation sequencing ( ... Load the array data. Load the genome sequence. Run Batman: Calibrate the Batman model: Before any data can be analysed, it is ... Register the array design: The array design (i.e. complete list of probes, with their genomic locations) should be provided as ... running Batman on a set of 100 Agilent Human DNA Methylation Arrays (about 250,000 probes per array) took less than an hour to ...
*  Association of Biomolecular Resource Facilities
Protein/Peptide Chemistry: amino acid analysis, N- and C-terminal sequencing, peptide synthesis, peptide/protein arrays. ... Mass Spectrometry: qualitative, quantitative, and structural analysis of proteins, carbohydrates, oligonucleotides, and lipids ... The next year protein sequencing and amino acid samples were sent to survey 103 core facilities. By 1989 the ABRF was formally ... ABRF Next Generation Sequencing Group (ABRF-NGS) Antibody Technology Research Group (ARG) Biomedical 'Omics Research Group ( ...
*  Representational difference analysis
... (RDA) is a technique used in biological research to find sequence differences in two ... This technology has been further enhanced through the development of representation oligonucleotide microarray analysis (ROMA ... which uses array technology to perform such analyses. This method may also be adapted to detect DNA methylation differences, as ... Genomes or cDNA sequences from two samples (i.e. cancer sample and a normal sample) are PCR amplified and differences analyzed ...
*  OLIGO Primer Analysis Software
Genome-Wide Oligonucleotide-Based Array Comparative Genome Hybridization Analysis of Non-Isolated Congenital Diaphragmatic ... Sequencing and in vitro Amplification of DNA; Nucleic Acids Research 17, 8543-8551. Wojciech Rychlik, William J. Spencer, and ... oligonucleotide-based array hybridization studies, degenerate primer studies, microsatellite analysis, DNA microarray detection ... OLIGO Primer Analysis Software was the first publicly available software for DNA primer design. The first papers describing ...
*  FlexGen
The FlexArrayer is also applicable for array based re-sequencing. The FlexArrayer provides microarray and oligopool synthesis ... Analysis of custom genomic regions of interest (e.g. specific genes, multiple variants and/or complete pathways). Analysis of ... Thus, the maximum length of any oligonucleotide produced on this platform is 60mer in length. The microarray is now ready to be ... Two European Labs Turn to Next-Gen Sequencing for BRCA1/2 Testing, INsequence, October 26, 2010. SM Carr et al., DNA "Re- ...
*  FnrS RNA
However, northern blot analysis of this 477bp sequence yielded no results. A subsequent tiling array analysis sequencing Hfq- ... "Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Res. 30 (17): 3732-8 ... "Inverse regulation in the metabolic genes pckA and metE revealed by proteomic analysis of the Salmonella RcsCDB regulon". J ... "A computational approach to identify genes for functional RNAs in genomic sequences". Nucleic Acids Res. 29 (19): 3928-38. doi: ...
*  BRCA1
... heteroduplex analysis (HDA) by multi-capillary electrophoresis or also dedicated oligonucleotides array based on comparative ... When this happens, it is difficult for the repair mechanism to "know" how to replace the correct DNA sequence, and there are ... "High-resolution oligonucleotide array-CGH applied to the detection and characterization of large rearrangements in the ... "Mutational analysis of BRCA1 and BRCA2 and clinicopathologic analysis of ovarian cancer in 82 ovarian cancer families: two ...
*  Oncogenomics
2003). "End-sequence profiling: Sequence-based analysis of aberrant genomes". Proceedings of the National Academy of Sciences ... 2003). "Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation ... 2004). "1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis ... This analysis validated the approach of whole cancer genome sequencing in identifying somatic mutations and the importance of ...
*  Molecular biology
Arrays can also be made with molecules other than DNA. Allele-specific oligonucleotide (ASO) is a technique that allows ... The membrane is then exposed to a labeled DNA probe that has a complement base sequence to the sequence on the DNA of interest ... PMC 3467903 . Tarca, Adi L.; Romero, Roberto; Draghici, Sorin (31 December 2016). "Analysis of microarray experiments of gene ... custom arrays, and arrays with larger spots on porous membranes (macroarrays). There can be anywhere from 100 spots to more ...
*  Extracellular RNA
... next-generation sequencing) lead to variations in DNA sequencing that allowed for high-throughput analyses of many genomic ... Unlike microarrays, RNA sequencing is not constrained by factors such as oligonucleotide generation, and the number of probes ... Micro RNA arrays have been used in exRNA studies to generate miRNA profiles of bodily fluids. The advent of massively parallel ... Among these DNA sequencing-derived methods is RNA sequencing. The main advantage of RNA sequencing over other methods for exRNA ...
*  Leroy Hood
... are covalently attached to the oligonucleotide primer for the enzymatic DNA sequence analysis. During the analysis, fragments ... Array analysis has become a standard technique for molecular biologists who wish to monitor gene expression. DNA ink-jet ... A series of analysis cycles is performed to identify a sequence, one cycle for each amino acid, and the cycle times were ... 30 March 2006). "Analysis of the DNA sequence and duplication history of human chromosome 15". Nature. 440 (7084): 671-675. doi ...
*  Beijing Genomics Institute
The algorithm, called SOAPdenovo, can assemble a genome in two days and has been used to sequence an array of plant and animal ... SOAPdenovo is part of "Short Oligonucleotide Analysis Package" (SOAP), a suite of tools developed by BGI for de novo assembly ... "BGI Offers Next-Gen Sequencing Service, Kicks Off 100-Genome Sequencing Project , In Sequence , Sequencing , GenomeWeb". ... "BGI to Sequence Tiger, Lion, and Leopard Species This Year , In Sequence , Sequencing , GenomeWeb". Archived from the original ...
*  Glossary of gene expression terms
When assembled into a two-dimensional array, see oligonucleotide array or microarray. Operon - a genetic unit for coordinating ... MIAMI defines it as "the nucleotide sequence present in a particular location on the array". A Reporter may be single-stranded ... In gene expression analysis, expression level refers to the amount of mRNA detected in a sample. FGED - Functional GEnomics ... It is an array of series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles ...
*  Annexin A7
2004). "Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Structural analysis of the protein suggests that Annexin VII is a membrane binding protein with diverse properties including ...
*  Suspension array technology
... which is affected by length and sequence of the oligonucleotide probe. Therefore, for every experiment, only one possible ... Thus, the measurement by flow cytometry represents a replicate analysis of each array element. Effective gathering of ... For example, the commercially available microsphere arrays from Luminex xMAPTM technology uses 10X10 element array. This array ... The direct DNA hybridization approach is the simplest suspension array assay whereby 15 to 20 bp DNA oligonucleotides attached ...
*  Escherichia coli sRNA
"Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Res. 30 (17): 3732-8 ... Esr41 sequence is not present in nonpathogenic E. coli K12, but the sRNA can induce cell motility in K12 as well, suggesting ... Deep sequencing of RNA expressed during chemical stress and high cell density fermentation discovered 253 novel intergenic ... A computational screen based on promoter sequences recognised by the sigma factor sigma 70 and on Rho-independent terminators ...
*  Transcriptomics technologies
"Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays". Nature Biotechnology. 18 (6): ... Both spotted oligonucleotide arrays and Affymetrix high-density arrays were the method of choice for transcriptional profiling ... Sequence reads are not perfect, so the accuracy of each base in the sequence needs to be estimated for downstream analyses. Raw ... Fluorescence intensities directly indicate the abundance of each sequence, since the sequence of each probe on the array is ...
*  Bioinformatics
... expressed cDNA sequence tag (EST) sequencing, serial analysis of gene expression (SAGE) tag sequencing, massively parallel ... of the functional elements of the human genome that uses next-generation DNA-sequencing technologies and genomic tiling arrays ... New physical detection technologies are employed, such as oligonucleotide microarrays to identify chromosomal gains and losses ... A variant of this sequence alignment is used in the sequencing process itself. Before sequences can be analyzed they have to be ...
*  Fluorescence in situ hybridization
Repetitive DNA sequences must be blocked by adding short fragments of DNA to the sample. The probe is then applied to the ... FISH allows the analysis of a large series of archival cases much easier to identify the pinpointed chromosome by creating a ... Each probe for the detection of mRNA and lncRNA is composed of 20 oligonucleotide pairs, each pair covering a space of 40-50 bp ... on microhole-array chips". 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society. p. ...
*  SNP array
An array containing immobilized allele-specific oligonucleotide (ASO) probes. Fragmented nucleic acid sequences of target, ... and Oligonucleotide Microarrays: A Platform Comparison based on Statistical Power Analysis". DNA Research. 14 (1): 1-11. doi: ... For example, SNP arrays can be used to study loss of heterozygosity (LOH). LOH occurs when one allele of a gene is mutated in a ... A SNP array can also be used to generate a virtual karyotype using software to determine the copy number of each SNP on the ...