881 results about "Genomic DNA" patented technology

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.

The invention discloses a specific molecular marker, primers, a method and application for genetic sex identification of siniperca chuatsi, the specific molecular marker has two sequences in male fish and has one sequence in female fish, the primers comprise an upstream primer F and a downstream primer R. The primers are adopted to carry out PCR amplification on genome DNA of the siniperca chuatsi to be detected, and the specific molecular marker is obtained. And identifying the genetic sex of the siniperca chuatsi according to an agarose gel electrophoresis detection result. The invention further discloses application of a reagent, a primer, a kit or a method for detecting the specific molecular marker in genetic sex identification of siniperca chuatsi, artificial breeding of the siniperca chuatsi or all-female breeding of the siniperca chuatsi. The siniperca chuatsi genetic sex identification method has the advantages that sex-related male and female differential fragments are found through combined comparative analysis of male and female genomes, primers are designed for amplification verification, only a small amount of DNA of a to-be-detected sample genome is needed as a template, the genetic sex of the siniperca chuatsi can be accurately, simply, conveniently, quickly and stably identified only through PCR and agarose gel electrophoresis, and the method is not limited by the development stage of the siniperca chuatsi.

The invention relates to an IGF2BP3 gene molecular marker primer related to pigeon weight traits and application of the IGF2BP3 gene molecular marker primer, and belongs to the technical field of biology. According to the invention, genome DNA of a to-be-detected pigeon is taken as a template, a specific primer is adopted to carry out PCR amplification on the genome DNA, then a PCR amplification product is subjected to Sanger sequencing and SNP molecular marker genotyping, and then pigeon body weight character selection is carried out. The weight of G / G genotype pigeons is higher than that of A / G and A / A genotype individuals, and the weight of A / G genotype pigeons is higher than that of A / A genotype individuals. By eliminating A / G and A / A genotype individuals and retaining G / G genotype individuals, the molecular marker has the beneficial effects that the molecular marker is used as a genetic marker for breeding pigeons, and the pigeons with large weight and uniformity are bred; the method can efficiently and quickly identify the weight traits of the pigeons, improves the uniformity of the weight of pigeons, provides a scientific basis for the early breeding of the pigeons, and better serves the breeding of the pigeons.

To provide a technique that enables direct seeding cultivation of seed potatoes in the field of production of sweet potato tuberous roots (sweet potato cultivation), which offers significant labor-saving benefits, wherein the technique enables efficient development of sweet potato plants having desired traits and exhibiting low enlargement of seed potatoes.SOLUTION: A method for identifying a sweet potato plant exhibiting low enlargement of seed potatoes, includes the steps of: detecting a nucleotide site indicating the "Kyushu 199-type variant allele" associated with a DNA marker from a genomic DNA of the sweet potato plant to be identified, with respect to "the DNA marker that shows relevance to the phenotype of low enlargement of seed potatoes" in the genomic DNA of sweet potato plants; and determining that the sweet potato plant to be identified is a sweet potato plant exhibiting low enlargement of seed potatoes if a nucleotide site indicating the "Kyushu 199-type variant allele" associated with the DNA marker is detected in the detection step.SELECTED DRAWING: Figure 2

The invention discloses a molecular marker, a primer pair, a kit and a method for identifying the size character of watermelon seeds and application, and belongs to the technical field of molecular marker-assisted breeding. The invention provides a molecular marker (as shown in SEQ ID NO.1-2), a primer pair (as shown in SEQ ID NO.3-4) and a kit containing the primer pair for identifying the size character of watermelon seeds in order to identify the size character of the watermelon seeds more quickly and more accurately in the watermelon seedling stage and realize watermelon germplasm resource screening and molecular assisted selection breeding. According to the identification method provided by the invention, the to-be-detected watermelon genome DNA is extracted in the seedling stage, so that molecular marker-assisted selection can be performed on the watermelon seed size character, the operation is simple and convenient, the breeding accuracy and efficiency are improved, the variety breeding period is shortened, and the variety breeding process is accelerated.

The invention provides a method for simultaneously detecting three hematogenous parasites based on RAA-LFS and application of the method. The method comprises the following steps: firstly, screening target genes of genomic DNA of specific amplified toxoplasma gondii, babesia and plasmodium and primers of the target genes; a primer and probe combination for specifically amplifying the 18s rRNA-1 gene of the toxoplasma gondii, the 18s rRNA-2 gene of the babesia and the 18s rRNA-3 gene of the plasmodium is determined; rapid multiple detection is completed in a reaction system by utilizing an RAA constant-temperature amplification technology, and a detection result is intuitively judged by combining a lateral flow chromatography test strip, so that the detection efficiency is greatly improved, and the result can be obtained in a short time. The RAA-LFS detection method provided by the invention has remarkable advantages in application scenes such as epidemic disease prevention and control or blood screening.

Methods, systems, and software for estimating circulating tumor fraction are provided. A first plurality of nucleic acid sequences for a plurality of loci in genomic DNA from a solid tumor sample is obtained. A second plurality of nucleic acid sequences for a plurality of cell-free DNA fragments obtained from a liquid biopsy sample from the same subject is obtained. One or more somatic mutations is identified in the first plurality of nucleic acid sequences. A variant allele frequency (VAF) is determined for each somatic mutation based on a frequency of the respective somatic mutation in the liquid biopsy sample and a frequency of the corresponding wild type allele in the liquid biopsy sample, thereby determining a set of VAFs. An estimate of the circulating tumor fraction for the test subject is determined based on the set of VAFs for the one or more somatic mutations.

The invention discloses an indel molecular marker for identifying color and luster of citrus peel in a seedling stage and application of the indel molecular marker. The corresponding sites of the indel molecular marker of the citrus are positioned in chr7: 18, 398, 798-18, 399 and 289 intervals of a chromosome 7 of an SWO3.0 reference genome; the genome DNA of the citrus seedling stage plant is used as a template, the Indel molecular marker is amplified through PCR, the citrus seedling stage plant can be divided into a homozygous insertion type, a homozygous deletion type and a heterozygous type according to a PCR amplification result, and the three types are associated with the color of the citrus fruit for identifying the color of the citrus peel, so that the early screening of the seedling stage target traits of the citrus breeding population is realized, and the early screening of the seedling stage target traits of the citrus breeding population is realized. The breeding period is remarkably shortened, the breeding cost is reduced, and important technical support is provided for citrus fruit color improvement breeding.

CRISPR-Cas systems have been engineered for various purposes, such as genomic DNA cleavage, base editing, epigenome editing, and genomic imaging. Although significant developments have been made, there still remains a need for new and useful CRISPR-Cas systems as powerful precise genome targeting tools. The invention disclosed herein comprises CRISPR-Cas based methods for high integration and expression efficiency of transgenes together with high post-transfection cell viability in eukaryotic cells.

The present application discloses a specific DNA fragment for sex identification of Pelteobagrus ussuriensis and a method for sex identification, specifically relating to the technical field of sex identification of Pelteobagrus ussuriensis. The above-mentioned identification method includes the following steps: Dissect 5 female and 5 male Pelteobagrus ussuriensis of a full-sib family to determine the physiological sex; respectively extract DNA from the muscles of female samples and male samples, construct a paired-end genomic DNA library with an insert fragment size of 300 bp, and perform high-throughput sequencing; based on the GWAS and Fst methods, identify that the sex chromosome of Pelteobagrus ussuriensis is chromosome 8, and then screen for Indels within the sex determination region on chromosome 8; screen a 601-bp male-specific DNA sequence and design and synthesize primers; use PCR amplification and agarose gel electrophoresis detection, and the result without specific bands is female, and the one with a 356-bp band is male. This scheme has the advantages of strong specificity, simple primer composition, and more intuitive identification of the sex of Pelteobagrus ussuriensis.

The invention discloses an engineering bacterium capable of efficiently degrading NP as well as a construction method and application of the engineering bacterium, and belongs to the technical field of wastewater treatment. The engineering bacterium is pseudomonas monteilii EBTRC-PM with an overexpressed ubiH gene, and the engineering bacterium is a pseudomonas monteilii EBTRC-PM The construction method comprises the following steps: designing a primer according to the genomic DNA of the pseudomonas monteilii EBTRC-PM, carrying out PCR to obtain a ubiH gene segment, carrying out homologous connection on the ubiH gene segment and a plasmid, replacing a T7 promoter of a reconstructed plasmid with a strong promoter P13, and finally transferring into the pseudomonas monteilii EBTRC-PM to obtain the engineering bacterium capable of efficiently inhibiting the toxicity in the NPEO degradation process, so that the NP degradation capability is greatly improved, and the engineering bacterium has the advantages that the construction is simple, and the construction cost is low. Good application prospects are realized in the field of wastewater treatment.

The invention discloses a tricholoma matsutake mushroom, which is classified and named as tricholoma matsutake mushroom 11, and is preserved in China Center for Type Culture Collection on March 24, 2025 with the preservation number of CCTCC NO: M 2025577. The molecular marker identification method comprises culture and collection of hyphae, extraction of genome DNA, DNA fingerprint PCR amplification and electrophoresis detection of PCR products. According to the method, the tricholoma matsutake mushroom 11 which inherits the advantage of high thermotype of two parents, is good in hypha temperature tolerance and high in vigor, is similar to tricholoma matsutake in sporocarp shape and is not opened is obtained by carrying out crossbreeding of the mushrooms and screening after mushroom cultivation and fruiting, and the tricholoma matsutake mushroom 11 has good development and application prospects.

The invention discloses a KASP molecular marker, a primer pair, a kit and a method for identifying sweet melon pericarp color traits and application, and belongs to the technical field of molecular marker-assisted breeding. The invention provides a KASP molecular marker (SEQ ID NO.1-2), a primer pair (SEQ ID NO.3-5) and a kit containing the primer pair for determining the pericarp color character of the sweet melon in order to identify the pericarp color character more quickly and more accurately in the seedling stage of the melon and realize screening of germplasm resources and molecular-assisted selection breeding of the germplasm resources, and provides the KASP molecular marker (SEQ ID NO.1-2) for determining the pericarp color character of the sweet melon, the primer pair (SEQ ID NO.3-5) and the kit containing the primer pair. According to the identification method provided by the invention, the to-be-detected muskmelon genome DNA is extracted in the seedling stage, so that molecular marker-assisted selection can be performed on the sweet melon peel color character, the operation is simple and convenient, the breeding accuracy and efficiency are improved, the variety breeding period is shortened, and the variety breeding process is accelerated.

The invention discloses an extraction method and application of high-molecular-weight turbellarian worm genome DNA, and belongs to the field of turbellarian worm genome extraction.The turbellarian worm genome DNA extraction is achieved by improving a lysate formula and removing ethylenediaminetetraacetic acid and increasing Mg < 2 + > on the basis of a conventional reagent in a classic Tris-HCl-phenol-chloroform method to inhibit activity of deoxyribonuclease II in a turbellarian worm body to inhibit degradation of genome DNA, and the high-molecular-weight turbellarian worm genome DNA is obtained. Meanwhile, ribonuclease A is added, RNA in cells can be degraded in the tissue cell digestion process, so that the step of two times of purification is omitted, the loss of DNA yield is reduced, experimental steps are simplified, especially the step of DNA purification is reduced, the problem of degradation in the extraction process of the turbellarian turbellarian worm genome DNA is solved, and the genome DNA yield (gt; 10 micrograms per turbellarian worm), and the turbellarian worm genome ultra-long sequencing or PacBio high-fidelity sequencing requirements are met.

The invention provides a PCR (polymerase chain reaction) method for rapidly screening effective donors for FMT (fibronectin) treatment of depression, which comprises the following steps: (1) collecting excrement samples of the donors, and extracting total microbial genome DNA (deoxyribonucleic acid) of the excrement samples; (2) designing six primer pairs according to a specific conserved sequence of a target strain; (3) taking the extracted donor excrement DNA as a PCR (Polymerase Chain Reaction) template, and adding a primer pair for amplification; (4) observing a PCR result through electrophoresis; and if each target band is positive in the PCR electrophoresis result of the donor sample, determining that the donor contains the target strain, and determining that the donor is an effective donor for FMT treatment of depression. The effective donor suitable for FMT treatment of depression is screened out by detecting whether the donor faeces contain three key probiotics closely related to depression symptom relieving or not, a basis is provided for microbial therapy of mental diseases such as depression, and important clinical application value is achieved.

The present disclosure relates to certain compositions, kits, devices, systems and methods, e.g., compositions, kits, devices, systems and methods for assessing methylation status, and / or assessing tissue and / or organ damage or toxicity in a subject. In particular aspects, provided herein are compositions, kits, devices, systems and methods for assessing tissue and / or organ damage or toxicity in a subject based on assessing methylation status of selected one or more tissue-specific or organ-specific target polynucleotide(s), e.g., one or more tissue-specific or organ-specific target genomic DNA sequence(s), from the subject.

The invention discloses a method for gene modification of aureobasidium pullulans, which belongs to the technical field of gene engineering, and comprises the following steps: determining a malic acid synthase gene, obtaining a malic acid synthase gene segment, searching a gene sequence of the malic acid synthase in the disclosed aureobasidium pullulans as a template on NCBI (National Center of Biotechnology Information), and carrying out gene modification on the malic acid synthase gene segment to obtain a malic acid synthase gene segment; the method comprises the following steps: respectively designing an upstream primer and a downstream primer, taking extracted genome DNA of aureobasidium pullulans M1 as a template, respectively carrying out PCR amplification and recombinant plasmid pUC57-PMA-ms construction and linearization treatment on the upstream primer and the downstream primer, and introducing the plasmid into the aureobasidium pullulans M1 to obtain an aureobasidium pullulans recombinant strain; according to the method, the polymalic acid synthetase gene (PMA-ms) on an aureobasidium pullulans genome is knocked out from aureobasidium pullulans, the yield of pullulan in the obtained recombinant plasmid M1-2 is about 39.11 g / L, and compared with an original strain M1, the yield of M1-2 is increased by 9.79 g / L, and the practical application prospect of the method is improved.

The invention discloses a method for identifying Yushan black pigs by adopting an SNP (Single Nucleotide Polymorphism) molecular marker technology, and particularly relates to the technical field of molecular detection.The method comprises the following steps: S1, sample preparation: collecting any one of ear tissues, tail tips or blood samples of to-be-detected pig individuals, and extracting to obtain genome DNA (Deoxyribose Nucleic Acid); the genome DNA is used as a template, amplification detection is conducted through a first primer pair, a second primer pair, a third primer pair and a fourth primer pair corresponding to the first SNP site, the second SNP site and the fourth SNP site, and the nucleotide sequences of the first primer pair, the second primer pair and the fourth primer pair are sequentially SEQ ID NO.5-SEQ ID NO.12. By detecting the specific single nucleotide polymorphic sites in the Yushan black pig genome and carrying out genetic typing comparison, the Yushan black pigs and the filial generation thereof can be quickly and accurately identified.

The invention discloses a primer of a molecular marker in close linkage with a wheat powdery mildew resistance gene PmCWI77849. The molecular marker is YTUSSR-86; the nucleotide sequence of an upstream primer of the molecular marker is as shown in SEQ ID NO: 1; the nucleotide sequence of the downstream primer is as shown in SEQ ID NO: 2; a primer of the molecular marker YTUSSR-86 is used for carrying out PCR (Polymerase Chain Reaction) amplification on to-be-detected wheat genome DNA (Deoxyribose Nucleic Acid), and the molecular weight of an obtained amplification product is 151bp, namely the molecular marker closely linked with the wheat powdery mildew resistance gene PmCWI77849. The molecular marker primer closely linked with the wheat powdery mildew-resistant gene PmCWI77849 provided by the invention can be used for rapidly and accurately detecting whether a wheat breeding material carries the anti-disease gene PmCWI77849 or not in a seedling stage, and is beneficial to shortening the breeding period, improving the breeding efficiency and accelerating the breeding process.

An engineered producer cell comprising an inactivating mutation in one or more endogenous REP binding sites is provided, as are methods for producing the engineered producer cell and using the engineered producer cell to produce a recombinant viral vector and reduce producer cell genomic DNA contamination of a recombinant adeno-associated virus vector preparation.

The present invention relates to methods and kits for the detection of 5-hydroxymethylcytosine (5hmC) and / or 5-methylcytosine (5mcC). In some embodiments, the present invention relates to methods and kits for detection of 5hmC and / or 5meC in nucleic acid (e.g., DNA, RNA). In some embodiments, the present invention relates to detection of 5hmC in genomic DNA, e.g., mammalian genomic DNA

The invention relates to a PDC (Polycrystalline Diamond Compact) cell carrying a bar code DNA (Deoxyribose Nucleic Acid) tag convenient to track as well as a preparation method and application thereof, and belongs to the technical field of The invention provides an isolated culture method of PDC primary cells, and provides a method for constructing recombinant PDC cells containing bar code DNA tags. According to the PDC primary cell culture system, the cell caking rate is reduced, the cell viability and the adherence rate are improved, and continuous passage to 20 generations or above can be achieved. The PDC primary cells faithfully retain the heterogeneity of clinical tumor samples in the aspects of mutation types, tumor generation and development mechanisms and the like. The bar code DNA tag introduced into the PDC cell can be detected by carrying out targeted sequencing and single cell RNA sequencing on a bar code DNA tag sequence in cell genome DNA, so that different clone groups reserved from PDX of the PDC cell line are conveniently distinguished and tracked in a high-throughput manner.

The invention discloses a reagent and a method for detecting low-frequency pancreatic cancer KRAS G12D gene mutation based on a Cas12a-Cas13a combined reaction system. The reagent comprises a single-stranded substrate DNA (Deoxyribonucleic Acid), a TRNA (Transcription Ribonucleic Acid), a 12CrRNA, a 13CrRNA, a 12Report and a 13Report; the single-stranded substrate DNA is derived from genome DNA of a to-be-detected sample, after the genome DNA of the to-be-detected sample is extracted, asymmetric PCR is carried out by utilizing a PCR primer pair, namely, the single-stranded substrate DNA is amplified and comprises wild type WT and mutant type MT; the mutant MT is completely matched with a recognition region of 12CrRNA, and a base mismatch exists between the mutant MT and a recognition region of 13CrRNA; a base mismatch exists between the wild type WT and a recognition region of 12CrRNA, and the wild type WT is completely matched with a recognition region of 13CrRNA; the TRNA is a pre-synthesized single-stranded RNA, has a base mismatch with a recognition region of the 12CrRNA, and is completely matched with a recognition region of the 13CrRNA; the 12Reporter is a DNA (Deoxyribose Nucleic Acid) probe of the FAM and BHQ double-standard genes, and the 13Reporter is an RNA (Ribonucleic Acid) probe of the FAM and BHQ double-standard genes. The nucleic acid cleavage activities of Cas12a and Cas13a are jointly utilized to realize multiple signal amplification, so that low-frequency detection of KRAS G12D mutation, which is simple to operate and low in cost, is realized.

The invention provides a kit for detecting TP53 gene mutation. The kit for detecting TP53 gene mutation provided by the invention can accurately detect six TP53 gene mutation sites, namely R175H, R249S, R282W, R248Q, R273H and G245S, in genome DNA to be detected at the same time through a multiple fluorescent PCR reaction system and a multi-channel fluorescent signal, can accurately detect the six mutation sites, has ultrahigh amplification efficiency, detection efficiency, sensitivity and specificity, and can be widely applied to detection of TP53 gene mutation. The genotype of a sample with the genome DNA content of 1 ng can be accurately detected, the operation is simple and convenient, and the cost is low.

This application relates to reagents and methods for analyzing associated nucleic acids. Specifically, reagents and methods are provided for analyzing nucleic acids (e.g., genomic DNA) of circulating particles (i.e., particles derived from blood). The method includes associating at least two target nucleic acid fragments of the circulating particles to produce a group of at least two associated target nucleic acid fragments. In the method, the target nucleic acid fragments can be associated by techniques such as barcoding, partitioning, ligation, and / or individual sequencing. Sequencing of the group of associated fragments provides a group of informationally associated sequence reads corresponding to the sequences of the fragments from a single particle.

To provide a technique for reducing the count of bacteria involved in mucin decomposition within the intestine, wherein the present invention allows inhibition of growth of intestinal microbes such as Ruminococcus gnavus, which can be involved in mucin degradation; and thus, it becomes possible to reduce mucin degradation within the intestine, thereby preserving the intestinal barrier function, and contributing to the maintenance or enhancement of host health.SOLUTION: Provided is an agent that comprises agaro-oligosaccharides as an active ingredient to inhibit the growth of intestinal bacteria having, in genomic DNA, a NanA gene composed of a DNA sequence having at least 45.6% sequence identity to Sequence No. 1 (NanA gene of Ruminococcus gnavus).SELECTED DRAWING: Figure 1

The invention discloses a method for detecting accessibility of space chromatin and application of the method. The method comprises the following steps: (1) slicing a tissue sample to be detected on a chip with spatial information; (2) fixing, permeabilizing and dyeing a tissue sample to be detected; (3) preparing fragmented genome DNA (deoxyribonucleic acid); (4) performing DNA hybridization based on a transfer mode; (5) carrying out connection and terminal repair reaction on the fragmented genome DNA by using DNA polymerase and DNA ligase; (6) denaturation and melting; and (7) sequencing. According to the method, the transcriptional activity state of chromatin can be reflected through chromatin accessibility sequencing analysis, staining imaging and chromatin accessibility information can be obtained on the same tissue slice at the same time without complex micro-fluidic equipment, experimental operation is easy, repeatability is high, and the analysis result is more remarkable.

The present disclosure provides systems and methods to detect somatic or germline variants by providing a predetermined genomic DNA (gDNA) to an assay mixture, and capturing a sample of a subject's genetic information using a DNA sequencer and detecting genetic variants from the genetic information. A mutation may then be classified as being from a germline source if gDNA derived molecules have lengths inconsistent with those expected from cell-free DNA (cfDNA) derived molecules.