ABSTRACT: Ligation probe pool was tested with different concentrations of synthetic dsDNA template molecules to determine analytical sensitivity of the method. Probes are ligated into circular molecules if their target sequence is present in the reaction. Ligated probes are then PCR amplified and the PCR products are hybridized to a microarray by tag sequences.
Project description:Hybridization of ligation probes to a zipcode (tag) microarray. The purpose of the experiment was to establish functionality and target specificity of the ligation probes by using pools of synthetic templates with all of the probes. The templates are 80-mer synthetic dsDNA molecules, each specific for a single probe. Each probe is a ssDNA molecule containing target recognition sequences, PCR primer binding sequences and a unique tag sequence. If a matching target sequence is present in the mixture, the probes is ligated into a circular molecule, which can be PCR amplified and hybrized on a microarray harbouring complementary tag sequences.
Project description:The aim of the study was to use microarray for profiling the microbiota in anaerobic digestion process. The probes are ssDNA molecules that are ligated into circular molecules if a complementary target sequence is present in the sample DNA. Ligated probes are PCR amplified with a labeled primer, and the amplicons are hybridized on DNA microarray by tag sequences.
Project description:This study in rats was designed to investigate whether whole rhye (WR) can influence the metabolism of n-3 and n-6 long-chain fatty acids (LCFA) and gut microbiota composition. For 12 weeks, rats were fed a diet containing either 50% WR or 50% refined rye (RR). Total bacterial DNA was extracted from fecal and cecal samples (n=5 per group). 16S PCR amplification was performed to assess the microbial diversity at the family level using the HuGChip. Amplified DNA was purified and labelled with either Cy3 or Cy5 dye and hybridized on the microarray. A 15 chip study was realized, each corresponding to hybridization with 250ng of labelled 16S rRNA gene amplicons from either mice fecal and cecal samples. Each probe (4441) was synthetized in three replicates.
Project description:Comparison of two different multiplex PCR primer pools in amplifying target HPV types from plasmid templates. Template concentrations are either 1 ng or 1 pg. Templates are detected by type-spcific LDR probes hybridized on microarray.
Project description:Comparison of two different multiplex PCR primer pools in amplifying target HPV types from plasmid templates. Template concentrations are either 10 pg or 100 pg. Templates are detected by type-spcific LDR probes hybridized on microarray.
Project description:PCR read-off microarrays: The ability to efficiently and economically generate libraries of defined pieces of DNA would have a myriad of applications, not least in the area of defined or directed sequencing and synthetic biology, such as protein engineering and aptamer library screening, but also in applications associated with encoding and tagging. By this approach DNA microarrays were used to allow the linear amplification off immobilized DNA sequences on an array followed by PCR amplification. Arrays of increasing sophistication (1; 10; 3,875; 10,000 defined sequences) were used to validate the process, with sequences verified by selective hybridization to a complementary DNA microarray and DNA sequencing. This technique offers an economical and efficient way of producing hundreds to thousands of specific DNA libraries, while the DNA-arrays can be used as factories allowing specific DNA oligonucleotide pools to be generated with or without masking.
Project description:PCR read-off microarrays: The ability to efficiently and economically generate libraries of defined pieces of DNA would have a myriad of applications, not least in the area of defined or directed sequencing and synthetic biology, such as protein engineering and aptamer library screening, but also in applications associated with encoding and tagging. By this approach DNA microarrays were used to allow the linear amplification off immobilized DNA sequences on an array followed by PCR amplification. Arrays of increasing sophistication (1; 10; 3,875; 10,000 defined sequences) were used to validate the process, with sequences verified by selective hybridization to a complementary DNA microarray and DNA sequencing. This technique offers an economical and efficient way of producing hundreds to thousands of specific DNA libraries, while the DNA-arrays can be used as M-^SfactoriesM-^T allowing specific DNA oligonucleotide pools to be generated with or without masking.
Project description:5'RACE sequencing of B-cell receptors from spleen samples of Atlantic cod. Both IgH and all isotypes of IgL were sequenced with C gene specific primers.
Project description:Hybridization of HPV genotype recognizing ligation probes to a zipcode (tag) microarray. The purpose of the experiment is to establish functionality and target specificity of the ligation probes by using a single template at a time with all of the probes. HPV plasmid DNA PCR products are used as templates for ligation probes. Each plasmid contains the full genome of a given HPV type. One type of plasmid is used per experiment to test the signals of all of the probes agains that template. 19 different plasmids are tested this way (i.e. 19 samples in the experiment).