Gene expression quantitative method and device

A gene expression and target gene technology, applied in the field of genomics and bioinformatics, can solve problems such as the need to improve labor efficiency, strong dependence on the integrity of CATG sites and reference genes, and the long time required for sequencing analysis, so as to improve the comparison Efficiency, simplification of the comparison process, and the effect of improving relevance

Active Publication Date: 2014-07-02
武汉华大智造科技有限公司
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Problems solved by technology

[0003] Chinese patent application (application number: 201110283718.2, name: a method for quantitative analysis of gene expression) discloses a method for quantitative analysis of gene expression based on the Illumina platform, which can overcome the impact o

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  • Gene expression quantitative method and device
  • Gene expression quantitative method and device

Examples

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Embodiment 1

[0018] In this example, RNA samples were used to construct a library. For RNA samples, use Human Tissue Mixture RNA Microarray Quality Control Standard (UHRR-MAQC, Universal Human Reference RNA-MicroArray Quality Control) and Human Brain Mixture RNA Microarray Quality Control Standard (HBRR-MAQC, Human Brain Reference RNA -MicroArray Quality Control), where the UHRR-MAQC standard was purchased from Agilent Technologies, Inc., and the HBRR-MAQC was purchased from Ambion. In other specific embodiments, other types of RNA standard products may also be used, or RNA standard products purchased from other companies may be used, which does not constitute a limitation to the present invention.

[0019] The process of constructing the library in this example is as follows: take a total RNA sample, dilute it with DEPC (diethyl pyrocarbonate, diethyl pyrocarbonate) water, mix well, denature at 65°C, and use dT (Dynalbeads Oligo) 25 The magnetic beads extract and purify the messenger RNA...

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Abstract

The invention discloses a gene expression quantitative method and device. The gene expression quantitative method includes the steps that read section sequences containing nucleotide sequence information are obtained; the read section sequences are compared with all reference genes to obtain the read section sequences with successful comparison; the read section sequences with the successful comparison are filtered, the read section sequences with the soft shear ratio larger than a first preset value, the sequence length smaller than a second preset value and the comparison score smaller than a third preset value are rejected, and the ratio which the number of basic groups with unsuccessful comparison accounts for the total number of basic groups of each read section sequence serves as the soft shear ratio; the comparison score is a numerical value determined according to the matching degree of each read section sequence and the reference genes and the length of each read section sequence; for the filtered read section sequences, target gene expression is quantified by using RPKM. The read section sequences are compared with the reference genes instead of existing reference genomes, the comparison process can be simplified, and comparison efficiency can be improved.

Description

technical field [0001] The invention relates to the technical fields of genomics and bioinformatics, in particular to a quantitative method and device for gene expression. Background technique [0002] Transcriptome sequencing technology (RNA-seq, RNA sequencing) is to measure the sequences of small RNA (Ribonucleic Acid, ribonucleic acid), mRNA and non-coding RNA, or some of them with high-throughput sequencing technology. There are currently several RNA-seq sequencing platforms, including Hiseq, Roche FLX, Illumina Solexa, ABI solid, etc. The sequencing principles of different sequencing platforms are different, but the sequencing steps basically include library preparation, polymerase chain reaction (PCR, Polymerase Chain Reaction) amplification, etc. Through RNA-seq, researchers can obtain the status of gene expression in organisms, and study the differences in gene expression levels of different individuals, different periods, and different forms of tissues. [0003] ...

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Application Information

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IPC IPC(8): G06F19/20
Inventor 黄文潘卢志远龚梅花章文蔚席凤韩鸿雁
Owner 武汉华大智造科技有限公司
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