13 results about "Genomic research" patented technology

The application discloses a long-read data robust variant detection method and system based on data quality improvement, and belongs to the technical field of gene sequencing and biological information analysis. The method of the application is aimed at the characteristics of long-read data, and first, preprocessing is completed through sequence filtering and base correction, and a three-dimensional outlier feature system of sequencing support intensity, mapping quality reliability and strand-specific bias is constructed. Based on the median absolute deviation algorithm, the features are standardized and outlier scores are generated, a double-threshold dynamic optimization mechanism is constructed, and high-confidence data is screened. The variant candidate regions are identified through multi-tool joint comparison, the SNP and Indel are typed through a deep learning model, and the reliability of the results is ensured through triple cross-validation. The method does not need to manually set a fixed threshold, effectively suppresses interference factors, balances detection accuracy, robustness and scene universality, and provides high-quality variant data support for clinical diagnosis and genomics research.

The application discloses a chrysanthemum constitutive high-expression promoter and application thereof in gene editing. The nucleotide sequence of the promoter CmUbi is shown as SEQ ID NO. 4. Through double luciferase reporter experiments and stable genetic transformation experiments, it is proved that the expression activity of the CmUbi promoter in chrysanthemum protoplast and callus is significantly higher than that of commonly used CaMV 35S, AtRPS5a and corn ZmUbi promoters. A CRISPR / Cas9 gene editing vector is constructed by using the promoter, and a key gene of branch of hexaploid chrysanthemum is edited BRC1b , and a plurality of allele simultaneous mutation complete editing strains are successfully obtained, and the number of branches of the mutants is significantly increased. The endogenous high-activity promoter of the chrysanthemum provided by the application effectively solves the problems of low expression activity of an existing heterologous promoter in the chrysanthemum and poor gene editing efficiency of a polyploid, and provides an efficient and adaptive expression regulation element for chrysanthemum molecular breeding and functional genomics research.

The invention provides a method and system for gene expression quantitative trait locus analysis, and relates to the technical field of genomics, the method comprises the following steps: carrying out sample and locus level quality control on input genotype data, and generating a standardized genotype matrix; performing standardization processing and low expression gene filtering on the input gene expression data to generate a standardized expression quantity matrix; performing principal component analysis according to the standardized genotype matrix to obtain a group structure covariable; carrying out implicit factor analysis on the basis of the standardized expression quantity matrix to obtain a technical batch effect covariable; quantitative character site correlation analysis is carried out through a standardized genotype matrix, a standardized expression quantity matrix, a population structure covariable and a technical batch effect covariable. The method is suitable for functional genomics research, complex disease genetic mechanism analysis and precision medical related functional genetic variation mining scenes.

The invention relates to a device and a method for eluting, purifying and recovering oversized DNA (deoxyribonucleic acid) based on pulsed field gel electrophoresis, which are used for efficiently recovering complete DNA molecules from hundred kb level to Mb level. The device comprises an electrophoresis protection chamber with a polygonal container structure and a sample recovery chamber, the side edge of the protection chamber is provided with a semi-permeable membrane for current to pass through, and the recovery chamber is detachably placed in the center and comprises the semi-permeable membrane; the detachable and replaceable magnesium sheet is arranged in the protection chamber and is used for ionizing magnesium ions to promote DNA (Deoxyribose Nucleic Acid) compression; the method comprises the following steps: preparing a biological sample into an agarose gel block, cracking and cleaning the agarose gel block, placing the agarose gel block in a device, and adding a recovery protection solution containing PEG; under the condition of pulsed field gel electrophoresis, DNA migrates out of a gel block and is combined with magnesium ions to be compressed into spheres, and the spheres are collected in a recovery chamber after charges are neutralized. Compared with the prior art, the method provided by the invention overcomes the defects of low product purity and tedious steps of a traditional recovery method, realizes high-purity and high-efficiency integrated recovery, and is suitable for genomics research and biotechnology application.

The invention relates to a method for rapidly carrying out BSA (Bovine Serum Albumin) gene localization by utilizing a space mutation mutant. The method comprises the following steps: firstly, carrying propagules such as seeds through an aerospace craft, and constructing a broad-spectrum mutant library by utilizing space environment mutagenesis; returning to the ground, culturing and screening M1-generation mutants with target excellent characters, and hybridizing / backcrossing with a wild type to construct a character segregation population; by adopting a group separation analysis (BSA) strategy, selecting phenotype polar differentiation individuals, and respectively mixing the phenotype polar differentiation individuals to form a high-value pool and a low-value pool; and finally, carrying out whole genome high-throughput sequencing on the double pools and the parents, rapidly locking a genome region linked with a target character by combining bioinformatics analysis such as SNP-index and the like, and verifying candidate genes through gene annotation, molecular marking and gene editing. According to the invention, the broad spectrum of space mutagenesis and the high efficiency of the BSA-seq technology are integrated, the period from mutation creation to gene identification is remarkably shortened, and an innovative technical scheme is provided for crop genetic improvement and functional genomics research.

The present invention relates to a method for preparing a single cell multi-sample multi-body library and a use thereof. The present invention relates to a method whereby an epigenome and a transcriptome can be simultaneously analyzed at a single cell level, and the principle of regulating the epigenome and the transcriptome has been identified. Accordingly, the present invention makes it possible to reduce reagent costs by about 1 / 10 compared to the prior art and simultaneously analyze six or more samples, thus being economical and having the advantage of being able to contribute to high-tech genomic research. According to the present invention, six samples can be simultaneously analyzed, and ATAC as an epigenome and 5 prime RNA information as a transcript can be simultaneously collected and used to clearly identify the starting point of gene expression that immediately responds to epigenetic changes.

The application discloses a base recognition method based on semiconductor SERS technology and belongs to the technical field of biomedical detection. The specific method comprises the following steps: step one, synthesis of TiO2 nanoparticles; step two, preparation of a TiO2 / 4-MBA system; and step three, base recognition detection. The TiO2 / MBA system can be used for accurate and rapid DNA base recognition, and the developed TiO2 / MBA system is simple to prepare and has excellent base test performance, and has a high market application prospect. The application not only provides a novel base detection method, but also has high sensitivity and selectivity, can recognize and detect four bases and the non-covalent interaction between the four bases and 4-MBA in two pH environments, and has a simple and rapid operation process. The application not only provides a new method for base analysis, but also provides technical support for early diagnosis of DNA related diseases, genomics research and development of molecular sensors, and has a wide application prospect.

The invention belongs to the field of bioinformatics and genomics, and discloses a method for rapidly and accurately predicting an intron splicing site of a target species. The method comprises the following steps: 1) obtaining a genome sequence and transcriptome sequencing data of a target species; 2) screening annotation genes and constructing a training set and a test set; 3) performing learning training on splicing site information by adopting a deep learning model architecture combining a convolutional neural network, a bidirectional long-short-term memory network and a self-attention structure; 4) performing bit-by-bit prediction on the input gene sequence by using the model obtained by training; and 5) judging the position of the splicing site according to the prediction score, and labeling and re-evaluating the abnormal or low-credibility splicing site. The calculation model provided by the invention can learn key sequence features at splicing sites, and can be extended to various species through transfer learning to realize high-precision introne boundary prediction. According to the method, the gene annotation efficiency can be remarkably improved, splicing abnormity caused by mutation can be accurately recognized, and the method has important application value for genomics research and gene function analysis and regulation.

The invention discloses a method for realizing wheat whole genome large-scale mutation and germplasm creation by editing repetitive sequences. CRISPR / Cas9 target sites with the copy number higher than 20,000 in wheat genomes are screened, tandem repeat sequences and dispersed repeat sequences are edited in a targeted mode, and heritable large-scale variation, chromosome structure variation and agronomic character variation of the whole genome scale are induced and generated in progeny plants. By editing repetitive sequences, large-scale mutation with chromosome and subgenome specificity can be realized, the created mutant library not only provides heritable variation mutant types different from those of traditional physical and chemical mutagenesis methods, but also generates materials such as chromosome aneuploidy (such as monosome, tetrasome and whole-arm deletion) and the like. And a unique genetic resource is provided for wheat functional genomics research and germplasm improvement.

This invention provides a method, tool, and application for improving the gene editing efficiency of *Eimeria tenella*. The *Eimeria tenella* strain with KU80 deletion is obtained by knocking out the KU80 gene in *Eimeria tenella* using a CRISPR-Cas9 gene editing system. Compared with existing technologies, the tool and method of this invention can significantly improve gene-targeted integration efficiency, significantly reduce random integration events of exogenous DNA, and improve the accuracy and stability of gene editing. It is a universal gene editing platform that can be widely applied to gene knockout, gene knock-in, and endogenous marker research. The strain using this tool can significantly shorten the screening cycle for positive recombinant strains, improve experimental reproducibility, and provide important technical support for functional genomics research on *Eimeria tenella*.

The invention relates to a method for genetic transformation by combining agrobacterium rhizogenes with paeonia lactiflora stem cuttage. The method comprises the following steps: (1) determining infection time; (2) selecting Chinese herbaceous peony plants; (3) selection of plasmids and agrobacterium rhizogenes; (4) preparing an infectious substance; (5) preparing an explant; (6) infecting the paeonia lactiflora stem explant; (7) preparing a cutting medium; (8) culturing root systems; (9) identifying a transgenic result; and (10) planting and maintaining the plants. According to the genetic transformation cultivation technology adopted by the invention, a tissue culture link can be skipped, paeonia lactiflora stalks can be directly infected in a non-sterile environment, then cutting slips with transgenic root systems are obtained through cuttage cultivation, the process operation is simple, the paeonia lactiflora stalk cutting slips are used as explants, agrobacterium rhizogenes are utilized to infect the explants, and the survival rate of the paeonia lactiflora stalks is improved. Fleshy roots with transgenic root systems are obtained after cuttage cultivation and have the potential of growing and developing into complete plants, and a foundation is laid for subsequent paeonia lactiflora molecular breeding and functional genomics research.

The invention discloses an analysis method for studying crop continuous cropping adaptability by integrating small RNA and DNA methylomics. The analysis method comprises the following steps: collecting wheat samples under W1 and WM conditions; identifying a 21-24nt-siRNA cluster under the conditions of W1 and WM; carrying out differential expression analysis on the 24-nt siRNA cluster; for differentially expressed 24-nt siRNA, a cluster overlapped with a differential methylation region DMRs is screened out, only pairs with a consistent regulation and control mode are reserved and are defined as RdDM acting sites, and then siRNA target genes are predicted. By means of the analysis method, differential expression siRNA under the continuous cropping condition of crops can be systematically identified; in combination with whole genome methylation data (WGBS), analyzing the relevance between the siRNA and a differential methylation region (DMRs); determining a key RdDM target gene and a functional pathway thereof; a siRNA-DNA methylation-gene expression multi-level regulation and control network is constructed, and a theoretical basis and an application basis are provided for crop continuous cropping adaptability and molecular improvement.