117 results about "Transcriptome profiling" patented technology

The invention provides a Beijing duck whole genome 60K SNP (Single Nucleotide Polymorphism) liquid phase chip, which comprises a reagent for detecting SNP sites, the SNP loci comprise highly selected SNP loci in identified Beijing ducks, Beijing duck production trait related genes obtained from transcriptome analysis and high-effect SNP loci in corresponding annotation files, and SNP loci which are mined according to existing GWAS research and are significantly related to production traits such as growth / body type of the Beijing ducks and potentially significantly related to the production traits such as growth / body type of the Beijing ducks. On the basis of large-scale meat duck groups in China, and on the basis of reasonably processed re-sequencing data and genetic typing, representative SNP and InDel loci are screened. The Beijing duck whole genome 60K SNP liquid phase chip can be used for Beijing duck genetic typing, auxiliary breeding, genetic relationship analysis, variety identification and the like.

The invention discloses a method for improving synthesis of sakuranetin from yarrowia lipolytica based on transcriptome analysis and application of the method, and belongs to the technical field of gene engineering. Target genes are analyzed and screened through transcriptome sequencing so as to find a method capable of improving sakuranetin synthesis, and the method specifically comprises the steps that an Illumina HiseqTM platform is used for conducting comprehensive transcriptome analysis on an original strain in the logarithmic phase by applying an RNA-seq technology, then transcriptome data are deeply analyzed through KEGG pathway analysis, and the sakuranetin synthesis can be improved. Therefore, the gene showing significant differential expression in the key path of sakuranetin synthesis is identified. And finally, carrying out free expression and integrated expression on the screened key target gene, and verifying the influence on the sakuranetin yield. Finally, a recombinant yarrowia lipolytica strain which is integrated with the YALI0C01859g gene and has high sakuranetin yield is obtained, and the titer of sakuranetin is increased to 344.0 mg / L.

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 application of a VvENO2 gene in regulation and control of plant fruit development, and belongs to the technical field of plant genetic engineering. In the early stage, hydrogen peroxide (H2O2) treatment can significantly promote maturation of grape fruits, and transcriptome analysis on the grape fruits treated by H2O2 discovers that the expression quantity of the VvENO2 gene is reduced. In order to further clarify the function of the VvENO2 gene in the plant fruit development process, a subcellular localization test and promoter activity analysis are carried out on the VvENO2 gene, it is proved that the VvENO2 gene is localized in a cell nucleus, a promoter of the gene can start GUS reporter protein, and the activity of the VvENO2 gene can be enhanced through ABA and H2O2 treatment. Further, transgenic arabidopsis thaliana and transgenic grapes are constructed, and phenotypic observation proves that the VvENO2 gene negatively regulates the maturation of plant fruits. The invention provides a new regulation and control site for breeding of early-maturing varieties of plants.

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.

The invention discloses an ITPR1 gene-based SNP molecular marker related to pig hypoxia sensitivity and application of the SNP molecular marker. The SNP molecular marker is located at the 1712th site of a nucleotide sequence of an ITPR1 gene promoter, a basic group is C or T, C is a dominant allele under a hypoxia condition, and the nucleotide sequence of the ITPR1 gene promoter is shown as SEQ ID NO.15. The invention further discloses a preparation method of the SNP molecular marker related to pig hypoxia sensitivity and application of the SNP molecular marker related to pig hypoxia sensitivity. Through high and low altitude transcriptome analysis of Tibetan pigs and a pig skeletal muscle satellite cell hypoxia model, it is found that the ITPR1 gene plays an important role in pig hypoxia resistance, and an ITPR1 gene promoter region is utilized to construct a dual-fluorescein reporter vector to determine an SNP site (g.1712Cgt; t). The invention provides the SNP molecular marker to assist the breeding method of the 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 discloses a gene screening method influencing drought adaptability of Hu sheep, and relates to the technical field of molecular breeding. The method comprises the following steps: step 1, selection and treatment of experimental sheep; step 2, transcriptome analysis; step 3, carrying out methylation analysis on the whole genome; and step 4, carrying out transcriptome and whole genome methylation conjoint analysis. The LOC121817420 gene is mined through a transcriptome and whole genome methylation method, the expression quantity of the gene in Hu sheep whole blood in two regions is detected through a real-time fluorescence quantification method, the expression quantity of the gene in Hu sheep in the Hetian region of Xinjiang is high, and it is proved that the gene is one of main candidate genes, different from Hu sheep in the Taihu Lake basin, of the Hu sheep in Xinjiang.

The invention belongs to the technical field of plant heredity and genetic engineering, and particularly relates to a cold-resistant and bolting-resistant related gene BraTZF3 of Chinese cabbage and application of the cold-resistant and bolting-resistant related gene BraTZF3. A stress-related transcription factor BraA01g008400.3 C is screened by combining a yeast stress library screening technology with transcriptome analysis, the stress-related transcription factor BraA01g008400.3 C belongs to a co-tandem C3H type zinc finger protein and comprises a C-x8-C-x5-C-x3-H zinc finger (ZNF) structural domain, and tests prove that the BraTZF3 is positively correlated to low-temperature stress response and cold resistance, and the BraA01g008400.3 C can be used for preparing the stress-related transcription factor BraA01g008400.3 C. According to the present invention, the BraTZF3 is subjected to heterologous overexpression to positively regulate the cold resistance and the bolting resistance of arabidopsis thaliana, such that the gene provides the positive regulation effect on the cold resistance and the bolting resistance of the plant, especially the Chinese cabbage, and the new tool and the new method are provided for improving the cold resistance and the bolting resistance of the crop by using the gene engineering means so as to provide the good practical application value;

The invention relates to the technical field of microorganism single-cell sequencing, in particular to a single-cell tissue in-situ sequencing method based on a Raman spectrum sorting technology. According to the method, position information of microbial single cells in tissues is reserved through tissue slices, the microbial single cells of the tissues in the slices are identified and sorted based on Raman spectra, required target single cells are obtained, labeling is performed without depending on a probe and the like, and therefore in-situ detection of the single-cell tissue level is achieved. And obtaining single-cell genome and single-cell transcriptome information. The required tissue slice does not need the steps of enzyme penetration, digestion, marking and the like, the microbial form is directly observed under a microscope, Raman sorting is carried out, and the operation is simple; by combining cell morphology and spectrum comparison, tissue microorganism single cells are accurately sorted, species are identified through transcriptome analysis, and microorganism single cell level gene transcription changes in the host-microorganism interaction process can be revealed.

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.

A system and method are provided for transcriptomic MRI (TMRI) analysis of a subject to determine diagnostic or prognostic information about the subject. The method includes accessing diffusion-weighted MR image data acquired from the subject, processing the diffusion-weighted MR image data using a multi-compartment model, and processing the diffusion-weighted MR image data using a radiomic analysis to generate texture features. The method also includes analyzing the texture features to determine diagnostic or prognostic information about the subject and generating a report communicating the diagnostic or prognostic information about the subject.

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 invention relates to a drug combination of annona squamosa lactone compounds and sorafenib (SF), which is characterized in that four common human hepatoma cell lines HepG2, HuH7, MHCC97H and HCCLM3 are used as research objects, and the drug combination effect among different components is evaluated by using an MTT (3-(4, 5-Dimethylthiazol-2-yl)-2, 3-diphenyltetrazolium bromide) method and Synergy Finder software. The combination of the compound and SF shows an obvious synergistic inhibition effect on the growth of hepatoma carcinoma cells, and meanwhile, the pharmaceutical composition can synergistically reduce the ATP level of the hepatoma carcinoma cells and induce hepatoma carcinoma cell apoptosis. Pharmacodynamic experiments show that the compounds annonacin and SF can synergistically inhibit tumor growth and induce tumor cell apoptosis, and have no obvious toxicity to normal organs of nude mice at a low dosage. In addition, transcriptome analysis predicts that the anti-liver cancer target of the annonacin is possibly related to the SLC33A1 gene. The method can be used for preparing anti-hepatoma drugs and researching related mechanisms. The annona lactone compound disclosed by the invention is derived from annona montana Macf. Which is an annona plant, namely annona montana Macf.

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 relates to the technical field of biology, in particular to application of osteopontin in regulation of intestinal anaerobic symbiotic bacteria colonization. The osteopontin is used for preparing food or medicine for improving the immunity of the intestinal tract, and the food or medicine is used for improving the abundance of anaerobic symbiotic bacteria in the intestinal tract; according to the application disclosed by the invention, firstly, by virtue of transcriptome analysis, it is proved that the abundance of Parabacteroids distans and Blautiapseudococcoids can be remarkably improved by virtue of the exogenous osteopontin, so that the abundance of the Parabacteroids distans and the abundance of the Blautiapseudococcoids can be remarkably improved; secondly, the invention also proves that the exogenous osteopontin can be used for inhibiting the proliferation of harmful bacteria Escherichia coli; therefore, the intestinal immunity is improved, the intestinal barrier is improved or repaired, and the intestinal flora balance is maintained. The composition is suitable for infants, old people, patients and other people with low immunity.

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.

The invention discloses an in-situ labeling method of living cell mitochondrial ribonucleic acid and application of the in-situ labeling method. The invention provides a methylene quinone precursor probe as shown in a formula (I) or a formula IX. Both the photosensitizer and the methylene quinone precursor probe have the properties of entering cells and enriching into mitochondria, and the methylene quinone precursor probe does not have the ability to bind with single-stranded nucleic acid. The method comprises the following steps: sequentially co-incubating test cells with a photosensitizer and a methylene quinone precursor probe, and irradiating by using light corresponding to an excitation wave band required by the photosensitizer, so that an azido phenyl protecting group of the probe is removed, and mitochondrial nucleic acid is combined with a methylene quinone intermediate, namely, the mitochondrial nucleic acid is labeled in situ by using the methylene quinone intermediate. After the marked cells are subjected to cell lysis and nucleic acid extraction, the marked nucleic acid can be enriched and purified through streptavidin magnetic beads for subsequent transcriptome analysis. # imgabs0 #

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.