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Oligonucleotide chip for detecting complete genome CpG island and uses thereof

An oligonucleotide and genome-wide technology, which is applied in the field of oligonucleotide chips to detect CpG islands in the whole genome, can solve the problems of inability to detect CpG sites and difficulty in large-scale whole-genome analysis

Inactive Publication Date: 2008-06-25
SHANGHAI BIOCHIP
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Although there are many DNA methylation detection technologies, each method has certain limitations, it is difficult to achieve large-scale and genome-wide analysis, and it cannot detect methylation or non-methylation in the whole genome. DNA-specific CpG sites

Method used

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  • Oligonucleotide chip for detecting complete genome CpG island and uses thereof
  • Oligonucleotide chip for detecting complete genome CpG island and uses thereof
  • Oligonucleotide chip for detecting complete genome CpG island and uses thereof

Examples

Experimental program
Comparison scheme
Effect test

preparation example Construction

[0023] (1) Preparation of oligonucleotide chips

[0024] 1) Probe design

[0025] Probes were designed for the CpG islands in the whole genome and the nucleotide sequence of the 2 kb region downstream of the CpG islands. On average, 6 to 10 probes were designed for each CpG island to determine the position of the CpG island where the detected DNA was located. The designed probe length is 30bp-55bp, the Tm value is 65°C-70°C, and the GC content is 50-60%.

[0026] 2) Chip preparation

[0027] It is carried out by in situ synthesis.

[0028] (2) Processing and labeling of samples to be tested

[0029] 1) Whole-genome DNA extraction and acquisition of target genes

[0030] Using the FlexiGene DNA Kit (250) (QIAGEN, Cat. No. 51206) kit to extract the genomic DNA of the sample to be tested. Transfer the extracted and dissolved DNA into a high-pressure sterilized 1.5ml centrifuge tube, take 1ul for electrophoresis (1% agarose gel, 0.5×TBE, EB, 80MV, 1.5 hours of electrophoresis...

Embodiment 1

[0041] The method for using the oligonucleotide chip of the present invention to detect human whole genome CpG islands is as shown in the accompanying drawings, and the specific steps are:

[0042] 1. Preparation of Oligonucleotide Chips

[0043] 1) Probe design

[0044] A total of 367,802 probes were designed for 46,957 CpG islands in the human genome and the nucleotide sequences of the 2kb region downstream of the CpG islands, and an average of 8 probes were designed for each CpG island to determine the location of the detected DNA. Location of CpG islands. The designed probe length is 30bp-55bp, the Tm value is 65°C-70°C, and the GC content is 50-60%.

[0045] 2) Chip preparation: in situ synthesis is used.

[0046] 2. Processing and labeling of samples to be tested

[0047] 1) Extraction of human genomic DNA and acquisition of target genes

[0048] Genomic DNA in human peripheral blood or tissues was extracted using the FlexiGene DNA Kit (250) (QIAGEN, Cat. No. 51206)...

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Abstract

The invention relates to a gene chip, and discloses an oligonucleotide chip for detecting a whole genome CpG island. The invention consists of solid-phase carriers and probes, wherein, the probes are hybridized with nucleotide sequences and / or complementary sequences thereof of the CpG island in the whole genome and 2kb areas of the upstream and downstream of the CpG island. The invention also discloses a method of detecting the position of the whole genome CpG island with the oligonucleotide chip. The oligonucleotide chip of the invention can carry out the CpG island detection of methylate and / or methylate DNA rapidly and accurately with high flux, and provides a powerful tool for correlation studies on the whole genome CpG island.

Description

technical field [0001] The invention relates to a gene detection chip, in particular to an oligonucleotide chip for detecting whole-genome CpG islands and its application. Background technique [0002] The function of normal cells is related to the genetic information, genetic regulation and epigenetic regulation of the cell itself. With the implementation of the Human Genome Project, the important role of the genetic information carried by the genome in the occurrence and development of diseases has been compared at home and abroad. Deep research. Relatively speaking, the important role of epigenetic information carried by chromatin in the occurrence and development of diseases has just begun to be recognized, and epigenetic genomes are emerging. Epigenetic processes including DNA methylation, histone modification and ATP-dependent modification of chromatin can cause changes in gene expression. Among them, methylation of DNA is a research hotspot at present. [0003] The...

Claims

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Application Information

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IPC IPC(8): C12Q1/68G01N21/64
Inventor 秦颖肖华胜
Owner SHANGHAI BIOCHIP
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