70 results about "Transcriptome profiling" patented technology

According to the screening method for the potential protein biomarkers and the drug targets of the gastric cancer, Mendel randomization analysis in a proteome range is adopted, the genetic causal relationship between circulating plasma protein and the risk of the gastric cancer is evaluated, and finally the remarkably related protein is identified. According to the screening method of the potential protein biomarker and the drug target of the gastric cancer, provided by the invention, the potential association between circulating plasma protein and the gastric cancer is systematically revealed by integrating Mendel randomization, single-cell RNA sequencing analysis, space transcriptome analysis, virtual drug screening, molecular docking, molecular dynamics simulation and other methods.

Provided herein are systems and methods for identifying a disease or disorder of a patient, identifying if a patient is likely to respond to a treatment for the disease or disorder, and / or predicting the clinical outcome of the disease or disorder of a patient. Systems and methods described herein may be directed to patients with different chronic conditions, inflammatory conditions, and / or autoimmune conditions. Systems and methods described herein may be directed to patients with a dermatological condition.

The invention discloses application of an MsGDSL1 gene in regulating and controlling the size and yield of plant leaves, and belongs to the technical field of plant genetic engineering. According to the invention, transcriptome analysis is utilized to clone an MsGDSL1 gene participating in regulation and control of the leaf size of medicago sativa. Experimental data show that compared with a wild control plant, the leaf area of an alfalfa MsGDSL1 gene overexpression plant is averagely enlarged by 60.54%, the fresh grass yield of a transgenic plant is averagely increased by 58.97%, and the hay yield is averagely increased by 61.88%; and the leaf area of an arabidopsis overexpression strain is averagely enlarged by 4 times compared with that of a wild type. The result further shows that the MsGDSL1 gene has cross-species high conservative property on the function of regulating and controlling the size of the plant leaf, and the core value of the MsGDSL1 gene in the yield improvement of the medicago sativa is proved.

The invention discloses a compound composition of fluopyram and dsRNA (double-stranded ribonucleic acid) and application of the compound composition in prevention and control of nematodes. The method comprises the following steps: soaking pine wood nematodes by adopting a fluopyram medicament with LC20 concentration, collecting samples at different time points respectively, and carrying out transcriptome analysis. The pesticide compound composition for effectively poisoning and killing the pine wood nematodes is obtained by comparing gene expression differences at different time points, screening out remarkably up-regulated detoxification genes BxCYP, BxCES and BxUDP, designing and synthesizing double-stranded RNA (ds BxCYP, ds BxCES and ds BxUDP) according to the detoxification genes, and compounding the double-stranded RNA with fluopyram. The pesticide compound composition has a remarkable synergistic prevention and control effect on pine wood nematodes, is expected to become a novel and efficient pine wood nematode prevention and control agent, and provides a new strategy and theoretical basis for prevention and control of pine wood nematode diseases.

The invention discloses application of an MsMYB-ZD gene in regulating and controlling the leaf size and yield of medicago sativa, and belongs to the technical field of plant genetic engineering. According to the invention, an MsMYB-ZD transcription factor for regulating and controlling the leaf size of medicago sativa is cloned by using transcriptome analysis; experimental data show that the MsMYB-ZD gene presents a gradually up-regulated expression mode in a leaf development process; compared with wild alfalfa Gongnong No.1 1-16 single plants, the leaf area of the overexpressed MsMYB-ZD transgenic single plant is averagely enlarged by 77%, and the expression quantity and the leaf area of the transgenic line show a remarkable positive correlation relationship; the fresh grass yield of a transgenic single plant is increased by 158.7%, and the hay yield of a single plant is increased by 207.5%. The results show that the gene has important significance for improving the yield of medicago sativa.

Inflammatory bowel disease (IBD) in humans and dogs and other companion animals is characterized by infiltration of lymphocytes and macrophages into the mucosa and submucosa and clinical signs of gastrointestinal (Gl) dysfunction (diarrhea, malabsorption, weight loss). Alteration of the gut environment and development of dysbiosis may allow the overgrowth of pathogenic bacteria and induction of intestinal injury and inflammation in IBD. What is needed are novel methods that allow for rapid diagnosis of IBD (and follow-up monitoring) and treatment of the disease. The present disclosure relates to methods for diagnosing and treating inflammatory bowel disease (IBD) or gastrointestinal lymphoma.

The use of different primer sets in reverse transcription incorporates tags allowing for the selective amplification of cDNA transcribed using the different primers. Primers targeting non-desired RNA sequences such as ribosomal RNA can be used to prevent subsequent amplification of cDNA transcribed from those non-coding fragments. Accordingly effective depletion of non-desired sequences after cDNA amplification can be achieved. Systems and methods of the invention have applications in whole-transcriptome analysis. Non-coding sequence targeting primers can include nucleotide analogs that, when enzymatically processed, prevent subsequent amplification. Library preparation can include single primer isothermal amplification (SPIA) techniques wherein an RNA sequence required for SPIA is included in random primers but is absent from primers targeting non-coding RNA.

In nerve diseases, cell dysfunction due to amyloid aggregate accumulation in nerve cells has attracted attention, but dysfunction of nerve axons responsible for neurotransmission is also considered to be one of the causes. However, no therapeutic agent that focuses on the repair and maintenance of nerve axons has been found. An object of the present invention is to provide a therapeutic agent that activates oligodendrocytes having a function of preserving nerve axons.SOLUTION: Transcriptome analysis with a psychotropic drug is carried out using an oligodendrocyte marker as an indicator, and it is found that the combined use of DPZ and NFN characteristically increases the expression of a transcriptional factor OLIG1 inducing the differentiation-maturation of the oligodendrocyte. Moreover, the drug concentration at this time was much lower than the expected clinical dose. The combined use of NFN and DPZ was observed to improve spatial memory in the mouse Y-maze test. The combination of NFN and DPZ can provide a novel treatment for cognitive and memory functions associated with neurological disorders.SELECTED DRAWING: None

The invention provides a peanut bacterial wilt resistant gene AhNHL24 as well as an identification method and application thereof, and belongs to the technical field of plant genetic engineering. The peanut disease resistance related gene AhNHL24 is separated from peanuts, the DNA sequence of the peanut disease resistance related gene AhNHL24 is shown as SEQ ID NO: 1, and the amino acid sequence of protein coded by the gene AhNHL24 is shown as SEQ ID NO: 2. According to the preparation method of the peanut disease-resistant gene, the AhNHL24 gene is separated and identified through Illumina RNA sequence and comparative transcriptome analysis, and transcription mode analysis and plant expression analysis find that the AhNHL24 gene can improve the resistance of plants to ralstonia solanacearum, so that the invention determines that the peanut AhNHL24 gene can be used as an important gene for peanut bacterial wilt resistance breeding.

Provided are a spatial transcriptomics chip, a preparation method therefor and the use thereof. The method comprises the following steps: cleaning a substrate, soaking same in a hydrophobic silane solution, then using a strongly corrosive reagent or a laser to etch same to form a dot array, and then sequentially adding a Spacer reagent and a Unylinker molecule for treatment; performing 3D inkjet printing or using a photochemical in-situ synthesis device to synthesize on the substrate a DNA sequence for spatial transcriptomics analysis; capturing the DNA sequence on the DNA array chip by using a gel or shrink film to obtain a gel layer or shrink film containing a captured sequence dot array; scaling down same at an equal proportion; and immobilizing the scaled-down gel layer or shrink film to the substrate, so as to obtain the spatial transcriptomics chip having high spatial resolution and high detection sensitivity. By means of the sequence dot array scaling-down process, the spatial resolution and detection sensitivity in spatial transcriptomics analysis are improved.

Methods of tagging cells with unique oligonucleotide “zipcode” constructs are provided. By these methods and associated compositions, cells in a multicellular structure such as a tissue section can be tagged with a construct, the unique composition of which is associated with the cells position in the multicellular structure. Subsequently, the multicellular structure can be dissociated into single cells and a single cell transcriptome analysis performed, as well as other types of single cell analyses. By preserving positional information in the analyzed single cells, biological processes within the tissue can be mapped. By these methods, the effects of the local environment surrounding a cell on its state and various functions can be elucidated, and intra-tissue processes can be mapped and observed. Likewise, coordinated actions by multiple cells within a tissue can be mapped and tracked over time.

The invention discloses a corn kernel linoleic acid content negative regulation gene ZmRPL31 as well as a mutant and application thereof, and a candidate gene ZmRPL31 closely related to linoleic acid anabolism in a high-linoleic acid corn selfing line YM-2 is successfully screened based on BSA (Bovine Serum Albumin) population construction and RNA-seq transcriptome analysis. Corn B73 pollen is treated through an ethyl methanesulfonate mutagenesis technology, and a rpl31 homozygous mutant strain is successfully constructed. GC-MS detection is carried out on the linoleic acid content of a homozygous mutant strain, and it is confirmed for the first time that the ribosomal protein gene ZmRPL31 has a negative regulation effect on synthesis of corn linoleic acid. Wherein the linoleic acid content of the rpl31-22 homozygous mutant strain in grain tissues is remarkably increased by 43.7% compared with that of wild type corn B73, and meanwhile, the linoleic acid content of the rpl31-22 homozygous mutant strain in leaves in the seedling stage is remarkably increased by 23.5% compared with that of the wild type corn B73.

The invention relates to the technical field of molecular biology and precision medical treatment, and relates to a molecular marker for predicting FOLFOX chemosensitivity and application thereof. A patient-derived colorectal cancer organoid biological sample library is constructed, the heterogeneity of in-vitro drug reaction is analyzed and evaluated through transcriptome, clinical groups sensitive to FOLFOX chemotherapy can be accurately recognized, a molecular marker prediction system containing 11 genes is obtained through further screening, and the molecular marker prediction system is used for predicting the FOLFOX chemotherapy. The method effectively overcomes the technical defect of lack of accurate prediction of colorectal cancer chemosensitivity at present, and has important value in the aspects of revealing disease mechanisms and guiding personalized treatment.

The application belongs to the field of genetic engineering and medical engineering, and discloses virK Application of gene in regulation of Klebsiella pneumoniae virulence. The application finds that the expression level of the gene is significantly increased in polymyxin-resistant mutant strains through transcriptome analysis, virK Further research shows that the expression of the gene is regulated by the PhoP / PhoQ two-component regulatory system. The application constructs virK Gene deletion mutant strains and complementary strains, and compares the virulence difference of the strains in an animal infection model, finds that virK The virulence of the deletion strain is significantly reduced, and the complementary strain can restore the virulence phenotype, indicating that virK The gene plays an important role in the regulation of Klebsiella pneumoniae virulence. The application first finds that PhoP can regulate virK Gene expression, and affects the virulence phenotype of Klebsiella pneumoniae through the regulation pathway, thereby revealing a new virulence regulation mechanism, and providing a theoretical basis for subsequent targeted intervention.

The invention discloses an RYR2-based SNP (single nucleotide polymorphism) molecular marker related to pig hypoxia tolerance and application of the RYR2-based SNP molecular marker, and the RYR2 gene is found to play an important role in pig hypoxia tolerance through high and low altitude transcriptome analysis of Tibetan pigs and a pig skeletal muscle satellite cell hypoxia model; a dual-fluorescein reporter vector is constructed by using an RYR2 gene promoter region to determine an SNP site (g.-565Agt; t). The invention provides a new SNP molecular marker to assist the breeding of hypoxia-resistant pig breeds, a large amount of group scale sampling and determination are not needed, and the breeding efficiency of the hypoxia-resistant pig breeds is effectively improved.

The invention provides research on a mechanism for regulating red bayberry fruit anthocyanin synthesis through optical signals and application of the mechanism. By treating Dongkui waxberries with different light-transmitting bags, the quality characteristics of mature fruits are analyzed, and comprehensive analysis is performed in combination with transcriptome and metabolome. The result shows that the bagging in the young fruit period significantly reduces the fruit quality, the black light-proof bag inhibits the fruit color change and anthocyanin synthesis, and the bagging influence in the color change period is small. Metabolome and transcriptome analysis shows that differential metabolites are enriched in anthocyanin synthesis and flavonoid metabolic pathways, related differential metabolites are identified, and core regulation transcription factors HY5 and DF1 participate in the photoregulation anthocyanin accumulation process. According to the invention, an optical signal regulation and control mechanism is defined, related factors and metabolites are identified, and a basis is provided for quality improvement and cultivation technology optimization of waxberries.

This invention belongs to the field of plant breeding and genetic engineering technology, specifically involving AtGalOxs Genes and their application in regulating plant organ size and development. Specifically, this invention screened a gene that regulates plant organ size and development. AtGalOxs It was identified as a key gene regulating the size and development of organs in Arabidopsis thaliana plants, and this was confirmed through cytological observation and transcriptome analysis. AtGalOxs Genes function by regulating cell proliferation and auxin signaling pathways, providing new theoretical basis for elucidating the molecular network regulating plant organ size; AtGalOxs The gene can be directly applied to the regulation of Arabidopsis plant architecture, and its homologous genes are conserved in crops such as Brassicaceae. This provides key gene resources for improving crop plant architecture and increasing yield, which is of great significance for promoting the development of plant molecular breeding technology and improving agricultural production efficiency.

The invention belongs to the technical field of space transcriptomics, and particularly relates to a method for identifying cell boundaries in space transcriptome analysis. Generally, when space transcriptome analysis is executed, the program roughly comprises sample preparation, optical structure image generation, space transcriptome information collection, optical structure image and space transcriptome information alignment and single cell injection translation. The method is characterized in that a specific fluorescent protein transgenic animal model is selected and matched with an optical and transcriptional image alignment method of the animal model, so that the structure and the outline of a single cell of a sample can be clearly seen under a fluorescence imaging system, and a fluorescence image can be obtained without penetrating through a cell membrane or cell nucleus for dyeing; therefore, the defect that the mRNA capture efficiency and the sample displacement are affected by the dye is avoided, the identification efficiency of the cell boundary is greatly improved, and the accuracy of follow-up algorithm assisted cell image cutting and large language model assisted cell translation is improved.

The application discloses a coronavirus transcriptome identification and analysis method, which comprises the following steps: using bwa software to perform sequence alignment on coronavirus second-generation sequencing original fastq files obtained from a short read archive SRA and NCBI reference genomes, to generate BAM files; calling and filtering single nucleotide polymorphisms SNPs through bcftools, and annotating the SNPs by using a vcf-annotator; performing CIGAR string analysis and breakpoint identification operations on the BAM files, to perform sgRNA identification; generating an expression matrix from the sgRNA identification result and performing transcriptome analysis. The application further discloses a coronavirus transcriptome identification and analysis system, which comprises a storage and a processor; the storage is provided with a computer program, and when the computer program is executed by the processor, the method described above is realized. The coronavirus transcriptome identification and analysis method and system provide a new cognitive means for coronavirus biology, and provide valuable resources for the development of future treatment methods.

The invention belongs to the technical field of plant molecular biology and plant genetic engineering, and particularly relates to a method for revealing a biosynthesis molecular mechanism of zanthoxylum bungeanum leaf terpenoids based on metabonomics and whole transcriptome analysis. Through multi-omics analysis on the Chinese prickly ash leaves, the terpenoids are determined to be main contributing substances of the fragrance of the Chinese prickly ash leaves. Key candidate regulatory factors are screened and identified in combination with correlation analysis of gene expression level and terpenoid content, and the factors may participate in synthesis regulation of zanthoxylum bungeanum maxim terpenoid. On the basis of the key candidate regulatory factors, a regulatory network involving 9 DEmRNAs, 8 DEmiRNAs, 8 DElncRNAs and 14 DEcircRNAs is constructed, lncRNA and circRNA in the network are competitively combined with miRNA, expression of the key candidate regulatory factors is regulated in a targeted mode, and then the key candidate regulatory factors cooperatively participate in synthesis regulation of the zanthoxylum bungeanum maxim terpenoid.

The present invention relates to the technical field of microbial single-cell sequencing and in particular to a single-cell tissue in-situ sequencing method based on Raman spectroscopy sorting technology. The method comprises: preserving the position information of microbial single cells in a tissue by means of tissue sectioning, and identifying and sorting the microbial single cells in the tissue in a section on the basis of Raman spectroscopy to obtain desired target single cells, without relying on labeling with probes and the like, thereby realizing in-situ detection of the single cells at the tissue level and obtaining a single-cell genome and single cell transcriptome information. The microbial morphology of the desired tissue section is directly observed under a microscope and Raman sorting is performed, without the need for steps such as enzyme penetration, digestion, and labeling, and thus, the operation is simple. The microbial single cells in the tissue are precisely sorted by means of the cell morphology and spectral comparison, and the species are identified by means of transcriptome analysis, so that the transcriptional change of genes at the microbial single-cell level during host-microbe interaction can be revealed.

The present disclosure relates to methods and compositions for the approximately simultaneous amplification of RNA / cDNA and genomic DNA. The present disclosure further provides methods of producing an RNA library for transcriptome analysis and a DNA library for DNA sequence variation analysis. The present disclosure further provides methods of identifying a DNA sequence variation or a transcriptome variation in a sample. Aspects of the present disclosure further relate to a DNA library or RNA library produced by the methods of the present disclosure.

The invention belongs to the technical field of plant breeding and genetic engineering, and particularly relates to an AtGalOxs gene and application thereof in regulation and control of size development of plant organs. Specifically, a gene AtGalOxs for regulating and controlling the size and development of the plant organs is screened and is clear as a key gene for regulating and controlling the size and development of the plant organs of arabidopsis thaliana, and cytological observation and transcriptome analysis prove that the gene AtGalOxs plays a role by regulating and controlling cell proliferation and auxin signal pathways, so that the gene AtGalOxs can be used for regulating and controlling the size and development of the plant organs of the arabidopsis thaliana. A new theoretical basis is provided for analyzing a molecular network for regulating and controlling the size of the plant organ; the AtGalOxs gene can be directly applied to plant type regulation and control of arabidopsis thaliana, and the homologous gene of the AtGalOxs gene has conservative property in crops such as cruciferae and the like, so that a key gene resource is provided for plant type improvement and yield increase of the crops, and the AtGalOxs gene has important significance in promoting development of a plant molecular breeding technology and realizing improvement of agricultural production benefits.

The present invention relates to a novel blood biomarker SH3PXD2B for diagnosing hepatitis B virus (HBV)-associated hepatocellular carcinoma and a use thereof. In order to identify a novel serum biomarker, transcriptome profiling including buffy coat WTS data was used to distinguish blood biomarkers specific to the caused of hepatocellular carcinoma Confirmation was made through validation using publicly available large-scale RNA-seq data, and qRT-PCR and AUC analyses were performed. Through this, it was confirmed that SH3PXD2B was upregulated exclusively in hepatitis B virus hepatocellular carcinoma in buffy coat transcripts, and qRT-PCR data demonstrated significant upregulation of SH3PXD2B in HBV-HCC. Therefore, SH3PXD2B is expected to be advantageously utilized as a blood biomarker for hepatitis B virus-associated hepatocellular carcinoma.

The invention provides a method for identifying limb regeneration heterogeneity between salamander and xenopus laevis, and relates to the technical field of biology. Comprising the following steps: respectively extracting samples of salamander and xenopus at different stages, and carrying out RNA extraction and high-throughput sequencing on the samples to obtain original data; evaluating the quality of the original data, performing quality control on the original data, and removing low-quality basic groups or linker pollution sequences; constructing a salamander reference genome index, comparing the quality-controlled data with a reference genome, and outputting comparison data; outputting an original count matrix from the comparison data, and calculating a TPM (Trusted Platform Module) value by using the original count matrix in an R language environment; using sequence alignment to extract common genes of the salamander and the xenopus; and performing principal component analysis and correlation analysis on the acquired data. Through transcriptome analysis and sequencing, the molecular mechanism of the limb regeneration capacity heterogeneity of the salamander and the xenopus laevis is analyzed, and guidance is provided for research of other regeneration capacities.

The application provides a method for screening soybean Cercospora sojina blight response genes based on transcriptome analysis, which comprises the following steps: selecting pods of soybean Cercospora sojina blight infected plants and healthy plants planted in the field, performing transcriptome sequencing, screening differential expression genes of soybean responding to Cercospora sojina blight, analyzing biological pathways of the differential expression genes in the Cercospora sojina blight infection process, performing protein interaction analysis, screening interaction core genes, comparing sequences, performing transcript from scratch assembly, analyzing differential variable splicing events and exon usage differences through integration analysis, analyzing post-transcriptional regulation network dynamic characteristics of key candidate genes of soybean responding to Cercospora sojina blight, and screening Cercospora sojina blight response genes of soybean. Four Cercospora sojina blight response genes of soybean are obtained, and expression characteristics in different soybean tissues are analyzed, which provides a theoretical basis for soybean Cercospora sojina blight resistance breeding.

The invention provides a primer and a method for detecting the expression characteristic of a papaya Pleurotus geesteranus transaminase gene. The sequences of the primers are as shown in SEQ ID NO. 1-2. Based on the primer, the invention establishes a fluorescent quantitative PCR method for detecting the change of the expression quantity of the transaminase gene after the papaya Pleurotus geesteranus eats two different hosts, namely papaya and potato. Through transcriptome sequencing verification, the gene expression trend obtained by the fluorescent quantitative PCR is consistent with the transcriptome analysis result. The invention lays an important foundation for exploring the influence of host conversion on the defense mechanism and transaminase gene expression characteristics of the papaya Pleurotus geesteranus.

The present application relates to the technical field of plant genetic engineering, and specifically provides the role of protein kinase gene GmCIPK6 in regulating soybean salt tolerance. The GmCIPK6 gene is cloned from soybean, and the GmCIPK6 overexpression and CRISPR / Cas9 knockout transgenic soybean plants are obtained by Agrobacterium-mediated genetic transformation technology. The results show that under salt stress, the leaf damage degree of the overexpression plants is significantly lower than that of the wild type, while the damage degree of the knockout plants is significantly aggravated; at the same time, the activities of antioxidant enzymes CAT, POD and APX in the overexpression plants are significantly increased, while those in the knockout plants are significantly decreased. Transcriptome analysis shows that the differentially expressed genes are significantly enriched in the hydrogen peroxide catalytic pathway and the oxidative stress related pathway. The present application confirms that the GmCIPK6 gene positively regulates the salt tolerance of soybean by regulating the antioxidant enzyme system, and provides an effective gene resource for breeding new salt-tolerant soybean varieties.

This invention discloses VvENO2 The application of genes in regulating plant fruit development belongs to the field of plant genetic engineering technology. Previous research in this invention found that hydrogen peroxide (H2O2) treatment significantly promotes grape fruit ripening. Transcriptome analysis of H2O2-treated grapes revealed… VvENO2 Gene expression levels decreased. To further clarify... VvENO2 The role of the gene in plant fruit development was investigated through subcellular localization experiments and promoter activity analysis, demonstrating its nucleus location and that its promoter can activate the GUS reporter protein. Furthermore, treatment with ABA and H2O2 enhanced its activity. In addition, transgenic Arabidopsis and transgenic grape were constructed, and phenotypic observations confirmed... VvENO2 Genes negatively regulate the ripening of plant fruits. This invention provides a new regulatory site for breeding early-maturing plant varieties.

The invention described herein provides an improved method and reagents to isolate nuclear RNA from high degradation tissues, such as duodenum, for use in, for example, high resolution transcriptome profiling and analysis.