401 results about "Transcriptome Sequencing" patented technology

The invention discloses a key gene identification method related to tobacco nitrogen response, which comprises the following steps: S1, setting four nitrogen fertilizer gradient treatments on the basis of same phosphorus and potassium fertilization by adopting a field experiment of a completely random block; s2, randomly taking the 6th to 8th leaves of the five plants in each area, and dividing a sample into two parts: quickly freezing one part with liquid nitrogen, and storing at-80 DEG C for RNA (Ribonucleic Acid) extraction and transcriptome sequencing; one part is used for measuring the nitrogen content, and after baking and drying treatment, a KjeltecTM8100 automatic nitrogen analyzer is used for measuring; s3, nitrogen content determination: determining the nitrogen content in the treated sample by using an automatic nitrogen analyzer KjeltecTM8100; according to the method, high-throughput transcriptome sequencing and weighted gene co-expression network analysis (WGCNA) are combined, so that not only can gene expression maps of flue-cured tobacco leaves treated by different nitrogen fertilizers be comprehensively captured, but also gene modules with similar expression modes can be mined from a global perspective.

The invention discloses a flavonoid glycoside glycosyltransferase LbUGT71BX1 in laportea bulbifera as well as the coding gene and the use thereof. The amino acid sequence of the flavonoid glycoside glycosyltransferase LbUGT71BX1 is shown as SEQ ID NO: 2. The nucleotide sequence of the coding gene of the flavonoid glycoside glycosyltransferase LbUGT71BX1 is shown as SEQ ID NO: 1. According to the invention, on the basis of relevant results of the second-generation transcriptome and the third-generation full-length transcriptome sequencing of the laportea bulbifera, the last-step key enzyme LbUGT71BX1 for the synthesis of the flavonoid glycoside in the laportea bulbifera is screened and identified by using a reverse genetics method, filling the terminal blank of the biosynthesis pathway of the flavonoid glycoside in the laportea bulbifera.

The invention discloses application of a cell surface adhesion molecule CD22 as a target spot in preparation of drugs for treating spinal cord injury related diseases. The change of gene expression in the glial scar formation process is represented by space transcriptome sequencing, and the specific expression of CD22 in the glial scar region is up-regulated. According to single cell sequencing, in-situ hybridization and immunohistochemistry, specific high expression CD22 of part of microglial cells in a glial scar area is found. CD22 is knocked out through a genetic means, and it is found that formation of glial scars after spinal cord injury is remarkably reduced through inhibition of CD22. Behavioral detection finds that the error rate of irregular horizontal ladders is remarkably reduced by inhibiting CD22, and fine movement recovery of hind limbs of mice after spinal cord injury is promoted. The siRNA specifically targeting CD22 is injected into the sheath, so that the expression of microglial cells CD22 is inhibited, the error rate of irregular horizontal ladders of hind limbs can be reduced, and the recovery of the fine movement function of the hind limbs of the mouse after spinal cord injury is promoted. The invention provides a new possibility for development of drugs for spinal cord injury and treatment of spinal cord injury.

The invention discloses a preparation method of fresh taxus chinensis stem and leaf protoplasts. The preparation method comprises a preparation process and a purification process. The preparation method of the taxus chinensis stem and leaf protoplast is simple and easy to operate, raw materials are easy to obtain and low in price, reagent components have good biocompatibility, and the taxus chinensis stem and leaf protoplast is free of harmful components, safe and environmentally friendly. The invention provides a simple and rapid taxus chinensis stem and leaf protoplast enzymolysis preparation method, which adopts vacuum filtration, accelerates the permeation of enzymatic hydrolysate and improves the enzymolysis efficiency, so that the protoplast can be rapidly obtained. Meanwhile, high-purity separation of the protoplast is carried out in combination with density gradient sedimentation of the iodixanol solution, so that the protoplast with uniform size and complete form is obtained, and convenience is provided for scientific researches such as subsequent conversion and single cell transcriptome sequencing.

The invention provides a nucleotide mutation site prediction model construction and disease-related point mutation identification method. Specifically, the invention provides a deep learning model-fused nucleotide mutation site prediction model construction method and a disease-related point mutation identification method. According to the method, DNA point mutation and RNA point mutation can be recognized from transcriptome sequencing data in a high-sensitivity and high-specificity mode, and basic data is provided for explaining mutation generation mechanisms and functions on the whole transcriptome and genome level.

The invention belongs to the technical field of biological medicine and molecular biology, and particularly relates to application of circ0005704 and related biological elements thereof in diagnosis and treatment of recurrent spontaneous abortion with unknown reasons. Researches find that differential expression and autophagy level of ULK1 in trophoblast cells of URSA patients are increased. High-throughput transcriptome sequencing is combined with bioinformatics analysis, and it is found that miR-26a-5p is down-regulated in URSA patients, is responsible for up-regulation of ULK1 and promotes autophagy of trophoblast cells, so that occurrence of URSA is increased. Through a high-throughput transcriptional set screening strategy and dual luciferase reporter gene analysis, it is found that circ0005704 enhances the expression of ULK1 through miR-26a-5p. In a word, the research of the invention shows that the circ0005704 / miR-26a-5p / ULK1 signal axis participates in the pathogenesis of URSA by adjusting the migration of the trophoblast cells, and a new target and scientific evidence are provided for the clinical treatment of URSA.

The invention belongs to the technical field of plant biology, and particularly relates to a gene for regulating and controlling powdery mildew resistance of cucumbers and application of the gene, two cswrky31 mutants are obtained based on a cucumber Tnt1 reverse transcription transposon mutant library, and the two cswrky31 mutants both show high susceptibility to powdery mildew bacteria. A target gene Csa5G551250 which is directly regulated and controlled by CsWRKY31 is screened by virtue of a high-throughput transcriptome sequencing technology and a DNA affinity purification sequencing technology in combination with a yeast one-hybrid experiment. A dual luciferase report experiment shows that the CsWRKY31 positively regulates and controls the expression of the Csa5G551250, and the overexpression of the Csa5G551250 gene promotes the resistance of the cucumber to powdery mildew bacteria. A new reference gene resource is provided for cultivation of cucumber disease-resistant varieties, and a new thought is provided for molecular mechanism research of transcription factor mediated plant immunity.

The invention belongs to the technical field of gene engineering, and particularly relates to application of corn zma-miR319 and / or a target gene of the corn zma-miR319 in regulation and control of corn stem rot resistance. According to the application, sequencing data of small RNA, a degradation group and a transcriptome are integrated, a miRNA family member zma-miR319 is identified, and the resistance of corn to stem rot can be positively regulated and enhanced; the target gene ZmMYB74 is a core regulation gene of an Fg response module, the stem rot resistance of a transgenic plant over-expressing the ZmMYB74 is weakened, and lignin deposition is reduced; the resistance is obviously enhanced by knocking out or inhibiting ZmMYB74, the ZmMYB74 is used as a transcription inhibition factor, the expression of a lignin synthesis related gene ZmCAD is negatively regulated and controlled, and the separation of the disease-resistant gene ZmMYB74 not only contributes to the cultivation of a persistent disease-resistant corn variety, but also deepens the understanding of a stem rot resistance molecular mechanism.

The invention relates to a training method of a respiratory tract infection disease progress and prognosis prediction model. The training method comprises the following steps: extracting mRNA from peripheral blood of a target patient, and carrying out transcriptome sequencing to obtain a sequencing result; based on the ferroptosis related gene set, comparing ferroptosis score differences of two groups of patients with community-acquired pneumonia and sepsis, and screening corresponding ferroptosis related genes with statistical significance from a sequencing result; screening out genes meeting preset conditions from the ferroptosis related genes based on LASSO regression; and establishing an RTI clinical outcome prediction model through logistic regression by taking whether the patient is sepsis or not as an outcome dichotomy variable and taking the screened gene expression quantity as a prediction variable. According to the invention, after the prediction model is subjected to machine learning screening such as LASSO and the like, the core feature with the highest prediction value is reserved, so that the risk of over-fitting of the model on training data is reduced.

The invention relates to a molecular typing model construction and identification method of BRCA mutation breast cancer. The method comprises the following steps: performing unsupervised clustering analysis on a gene with most significant change in a common transcriptome expression profile of BRCA1 / 2 mutant breast cancer to obtain an optimal clustering number, and dividing the optimal clustering number into subtypes with different clinical prognosis and molecular characteristics of the optimal clustering number; based on the clustering result, a random forest algorithm is utilized to construct a molecular typing model, the model comprises a plurality of key classification genes, and the molecular typing model is verified through a verification set and an external data set so as to ensure the accuracy, the stability and the clinical applicability of the molecular typing model. Molecular typing can be rapidly and accurately carried out according to common transcriptome sequencing data of a BRCA1 / 2 mutant breast cancer patient tumor sample, and a scientific basis is provided for selection of an individualized treatment scheme.

The invention discloses a rape grain weight regulation gene NGAL3 based on whole genome screening and a breeding application thereof, based on the seed size and grain weight phenotypic value of a cabbage type rape germplasm resource, a candidate gene interval is positioned by using GWAS; the method comprises the following steps: selecting large-grain-weight and small-grain-weight extreme phenotypic materials, performing transcriptome sequencing in a critical period of seed development, and screening differential expression genes; and performing cross comparison on the GWAS candidate gene and the differential expression gene to obtain a key gene for jointly regulating and controlling the size and the grain weight of the seed, and performing functional verification on the key gene. The thousand seed weights of the created homozygous three mutant strains L1-sg1-1-4-5 and L2-sg1-4-8-16 are obviously increased by 46% and 29% compared with those of the wild type strains. The invention provides a new target for high-yield rape breeding, and non-transgenic high-grain-weight germplasm can be created through gene editing or beneficial allelic variation of NGAL3 is selected and enriched under the assistance of molecular markers.

The invention relates to a method for screening drought-resistant tea germplasm and application. The method for screening the drought-resistant tea tree germplasm comprises the following steps: step 1, performing repeated drought treatment on a tea tree, and measuring phenotype, metabolome data and transcriptome data of a sample; 2, screening the differential metabolite from the metabolome data, wherein the expression mode of the differential metabolite is that the differential metabolite does not respond or has no significance in response when the differential metabolite is subjected to drought for the first time and has significant response after multiple times of repeated drought, and taking the differential metabolite as a memory metabolite; 3, screening and analyzing differential genes in the tea trees subjected to repeated drought treatment: screening memory key genes from the differential genes; and step 4, according to the transcriptional level of the memory key genes in the tea tree leaves, determining the key genes with high transcriptional level as the drought-resistant tea tree germplasm. The 9 memory key genes are verified, the result shows that the selected gene is consistent with the transcriptome sequencing result, and the gene has good sensitivity, specificity and accuracy in screening drought-resistant tea trees or improving the drought resistance of the tea trees.

The invention provides a construction method of a plant tissue space transcriptome sequencing library, which comprises the following steps: fixing and embedding plant tissues to obtain embedded blocks; performing autofluorescence detection and tissue permeabilization treatment on part of the embedded blocks, and determining an autofluorescence threshold value and target tissue permeabilization time; slicing, pasting and fixing the remaining embedding blocks, and performing microscope fluorescence scanning detection and tissue permeabilization treatment on the tissue-containing chip according to an autofluorescence threshold value and target tissue permeabilization time to obtain a permeabilized tissue chip; and carrying out reverse transcription, tissue removal, cDNA release, recovery and amplification on the permeabilized tissue chip to obtain a cDNA amplification product. The plant tissue transcript constructed by the construction method is not easy to diffuse and high in capture rate, high-quality in-situ capture time-space group data can be obtained, the accuracy and the credibility are high, the sequencing accuracy is ensured, and the application value is high.

The invention relates to the technical field of biomarkers, in particular to a biomarker composition for diabetic foot ulcer and application of the biomarker composition. The invention provides a biomarker combination for diabetic foot ulcer. The biomarker combination comprises a DDIT4 gene and a PKM gene. According to the invention, by integrating transcriptome sequencing data and single cell sequencing data, biomarkers DDIT4 and PKM closely related to diabetic foot ulcer (DFU) are successfully screened out. The expression of the two genes in a disease group is remarkably up-regulated, and the two genes are stably expressed in different data sets, so that a reliable molecular target is provided for early diagnosis of DFU.

The invention discloses a screening method of high-specificity variable splicing, which comprises the following steps: by taking transcriptome sequencing data (RNA-seq) of a target group and a control group as an analysis object, carrying out data processing, and then preliminarily detecting and identifying various types of candidate variable splicing events; carrying out multi-dimensional verification on the variable splicing event to obtain a high-credibility event; performing dual verification of multiple data sets on the screened high-credibility events to obtain high-credibility and high-stability events; and carrying out inter-group specific variable splicing screening to finally obtain a high-specificity event. By adopting the screening method disclosed by the invention, the variable splicing events with high accuracy, high inter-group specificity and high data reliability can be obtained, so that the workload of subsequent related research work is reduced.

The invention belongs to the field of biotechnology and medical technology, and discloses application of tumor-associated macrophages with high expression of SLC16A10 in prognosis diagnosis and treatment of colorectal cancer. According to the invention, colorectal cancer single-cell transcriptome sequencing data analysis before and after anti-PD-1 treatment is carried out in the earlier stage; the tumor-associated macrophage subgroup with high expression of the SLC16A10 is enriched in a response group after colorectal cancer anti-PD-1 treatment, and the prognosis of a colorectal cancer patient with high expression of the SLC16A10 is good. Knock-down of the SLC16A10 leads to reduction of expression of the macrophage M1 type marker, and activation and toxicity of co-cultured T cells are reduced. The SLC16A10 promotes T cell activation and weakens immunosuppression on T cells, so that colorectal cancer anti-PD-1 treatment response is caused. The research explains the influence and mechanism of the macrophage SLC16A10 on colorectal cancer anti-PD-1 treatment, and provides a new strategy and theoretical basis for immunotherapy of colorectal cancer.

The present application provides an application of inhibiting or knocking out tobacco polyphenol oxidase gene NtPPO12 in inhibiting tobacco browning. The present application screens an important gene NtPPO12 related to tobacco browning through transcriptome sequencing and molecular biology experiments, further verifies the promoter activity and gene expression site of NtPPO12, and deeply researches the function of the gene through gene editing and overexpression. The present application proves by molecular biology experiments that the NtPPO12 gene provided by the present application is a key gene related to browning in the mature curing process of tobacco, and by regulating the expression amount of the NtPPO12 gene, the browning degree of tobacco can be controlled, and the tobacco maturity and curing resistance can be improved, which is beneficial to reducing the picking frequency, improving the curing characteristics, and improving the appearance and internal quality of tobacco leaves, so it has a broad market application prospect.

The invention discloses a key gene AaMYB114 closely linked with the color character of an actinidia arguta fruit and application of the key gene AaMYB114. The AaMYB114 gene disclosed by the invention is positioned at 5237694-5239966bp of a chromosome 9 of an actinidia arguta genome, and the full length of the AaMYB114 gene is 2273bp. According to the application, all-red type and all-green type actinidia arguta are used as materials for transcriptome sequencing, and the gene AaMYB114 related to the formation of the peel color of the actinidia arguta is explored. Instantaneous conversion of the actinidia arguta fruit proves that the overexpression of the AaMYB114 increases the anthocyanin content in the actinidia arguta peel. Yeast one-hybridization and dual-luciferase report tests prove that the AaMYB114 not only interacts with a promoter of AaGST, activates the expression of the promoter and regulates anthocyanin transport of peel tissues of actinidia arguta, but also is combined with promoters of anthocyanin synthesis structural genes AaPAL, AaCHI and AaF3H and activates the expression of the promoters to promote anthocyanin synthesis. Therefore, the AaMYB114 gene plays a dual regulation and control role in the formation of peel color and luster, and can be used for cultivating red-peel actinidia arguta.

The invention discloses application of an Hspa5 inhibitor in preparation of a medicine for preventing or treating anxiety disorder. An anxiety mouse model is constructed through chronic constraint stress (CRS), and in combination with medial amygdala kernel (MeA) transcriptome sequencing and qPCR verification, it is found that the endoplasmic reticulum molecular chaperone Hspa5 is remarkably up-regulated in the anxiety state. Furthermore, an Hspa5 specific inhibitor HA15 is locally injected into a MeA brain region, so that the anxiety-like behavior induced by the CRS is remarkably improved, and the exploration time of an open field experiment central region, the exploration time of an open arm of an elevated cross labyrinth and the exploration time of a bright box of a bright-dark box experiment are prolonged. The invention discloses the function of Hspa5 as a novel anti-anxiety target for the first time, and provides a direct experimental basis and a transformation direction for developing a novel anti-anxiety drug which is non-monoamine and targets an endoplasmic reticulum homeostasis.

The invention belongs to the technical field of biological detection, and discloses a screening method of respiratory tract infection related biomarkers based on metatranscriptomics. Respiratory tract infection samples with different clinical phenotypes are subjected to metatranscriptome sequencing, data quality control, comparison and transcript quantification, pathogen and host information is reserved, then genes which are stably expressed or remarkably changed in different groups are identified by combining differential expression analysis and co-expression analysis, and potential biomarkers are obtained. And taking an intersection gene of three machine learning algorithms including an LASSO algorithm, a random forest model and an SVM model to obtain the biomarker. The invention provides a biomarker screening method for rapid and accurate identification of respiratory tract infection.

The invention provides a mechanism for regulating and controlling AsA content of kiwi fruits by AcMYB73 and AcMYB108 transcription factors and application of the mechanism. According to the application disclosed by the invention, after GABA is used for treating kiwi fruits, transcriptome sequencing is carried out, and AcMYB73 and AcMYB108 transcription factors which are most likely to regulate and control ascorbic acid-related metabolic genes are screened from numerous transcription factors with most obvious abundance change; experiments such as LUC / REN dual luciferase, yeast single impurity, gel migration and the like prove that both the AcMYB73 and the AcMYB108 can positively regulate and control the ascorbic acid synthesis gene and the circulating gene of the kiwi fruit and reversely regulate and control the ascorbic acid degradation gene of the kiwi fruit at the same time. The invention also successfully constructs overexpression vectors and interference vectors of AcMYB73 and AcMYB108, and successfully realizes regulation and control of the content of ascorbic acid in kiwi fruits.

Provided are a high-throughput transcriptome sequencing-based IKZF1 gene exon deletion recognition system and method. The exon deletion recognition system is obtained by inputting the number of IKZF1 exon junctions, differential genes and expression quantities thereof, and IKZF1 exon and intron mutation frequency information of samples as features into a constructed random forest model and performing prediction, and can be used for accurately predicting and recognizing any exon deletion with high accuracy and high specificity, providing guidance for patient prognosis and treatment.

The invention belongs to the field of genetic engineering, and relates to a mung bean VrLAL1 (LANCEOLATE LEAVES1) protein, a mung bean VrLAL1 gene and application of the mung bean VrLAL1 protein and the mung bean VrLAL1 gene in regulation and control of leaf size and pod length, M5311 wild species and al1 mutant species are hybridized, and the VrLAL1 gene is finely positioned on the basis of an existing mung bean molecular marker. The method comprises the following steps: selecting a plurality of candidate genes in a candidate interval, simultaneously performing transcriptome sequencing analysis on a mutant, screening and identifying a plurality of candidate genes in the candidate interval according to a transcriptome result, finding a mutant gene VrLAL1 gene, designing a primer, and performing PCR (Polymerase Chain Reaction) first cloning to obtain the VrLAL1 gene. The VrLAL1 gene has an obvious effect on regulation and control of organ size, leaf development and pod development, and can be used for variety improvement of legume crops.

The application discloses a kind of marker for predicting oocyte copy number variation and application thereof, the marker includes the combination of CLEC11A, P4HB, EFEMP2, IL32, FTL, FLNA, COL6A3, ACPP and APOO protein.By the marker of the application, the expression level of granulosa cell secretory protein can be determined by granulosa cell transcriptome sequencing, and the genomic CNV condition of corresponding oocyte can be inferred.The detection object of the technical solution is discarded granulosa cell in assisted reproductive technology, so it will not have any impact on oocyte, and it is non-invasive;The present study is a transcriptome and methylation group detection from single cell level, with high-throughput characteristics, and all granulosa cells and oocytes are one-to-one matched, which can reflect the difference between single cell level COCs.

The invention discloses a nuclear factor YB subunit gene GhNF-YB3 and application thereof. The nucleotide sequence of the gene GhNF-YB3 is shown as SEQ ID NO. 1, and the nucleotide sequence of the gene GhNF-YB3 is shown as SEQ ID NO. The site gene GhNF-YB3 significantly related to the cotton yield trait is obtained by performing yield trait investigation on 245 upland cotton varieties and combining population genome re-sequencing and ovule transcriptome sequencing one day after flowering to perform GWAS and eQTL positioning. Gene expression of the gene GhNF-YB3 is in significant positive correlation with two yield traits, namely seed index and boll weight, and the gene GhNF-YB3 may be a causal gene for regulating and controlling the traits of the seed index of cotton. The nuclear factor YB subunit gene GhNF-YB3 disclosed by the invention can be applied to identification of high-yield upland cotton varieties and improvement of cotton yield traits.

The application belongs to the technical field of biological detection, and discloses a screening method of respiratory tract infection related biomarkers based on macro-transcriptomics. The application performs macro-transcriptome sequencing on respiratory tract infection samples with different clinical phenotypes, performs data quality control, alignment, transcript quantification, retains pathogen and host information, and then identifies genes stably expressed or significantly changed in different groups by combining differential expression analysis and co-expression analysis, obtains potential biomarkers, and obtains the biomarkers by taking the intersection genes of three machine learning algorithms of LASSO algorithm, random forest model and SVM model. The application provides a screening method of biomarkers for rapid and accurate identification of respiratory tract infection.

The invention discloses siRNA capable of knocking down Pr18a9 gene expression and application of the siRNA, and relates to the technical field of biological medicine. The invention provides a positive-sense strand sequence and an antisense strand sequence of the siRNA, and the siRNA is used for preparing a preparation for promoting Schwann cell survival. According to the invention, the Prl8a9 gene of SCs is knocked down by virtue of a small interfering RNA technology; by improving the proliferation and migration capabilities of the Schwann cells, the apoptosis rate of the Schwann cells is reduced, and the survival rate of the Schwann cells is further improved. Meanwhile, a transcriptome sequencing technology is applied, key genes and pathways of Schwann cells treated by siPr18a9 are deeply excavated, and a theoretical support is provided for research on a repair mechanism after peripheral nerve injury.

The invention discloses a black fungus AMY protein and a coding gene and application thereof, and belongs to the technical field of protein engineering. The invention provides a black fungus AMY protein as well as an encoding gene and application thereof in order to excavate a key enzyme gene of a starch sucrose metabolic pathway in black fungus, and discovers and verifies that the black fungus AMY protein and the encoding gene thereof play a key regulation and control role in inducing synthesis of black fungus alpha-amylase through transcriptome sequencing. A solid foundation is laid for deeply exploring the function of a key gene of a starch sucrose metabolic pathway.

The application provides a WNT5B-promoting tooth differentiation biological product and an application thereof. Compared with the prior art, the application has the following advantages: the patent integrates human embryonic tooth germ spatial transcriptome sequencing and epithelial cell and interstitial cell extracellular protein group sequencing data, screens signal molecules WNT5B and CTNNB1 secreted in the development process of tooth germ epithelium, and confirms the important role of WNT5B protein in tooth germ development for the first time. Compared with other WNT family members, WNT5B has stronger tooth-forming ability of promoting tooth-derived stem cells; the effective concentration of WNT5B is low, and 10 ng / ml is the optimal concentration of WNT5B for promoting tooth-derived stem cells to form teeth; and the role of WNT5B and CTNNB1 in extracellular secretion of tooth germ epithelial cells and the synergistic effect of WNT5B and CTNNB1 in promoting tooth differentiation of tooth germ mesenchymal cells are further determined, that is, the combined low-concentration use effect of the two is better than the single high-concentration use.

The invention discloses a method for regulating and controlling the growth of mammary epithelial cells of milk goats based on a KLC1-chi-miR-423-5p-PDGFAceRNA network, and belongs to the field of animal molecular biology and cell biology. Through combination of transcriptome sequencing and functional verification, it is revealed for the first time that KLC1 can be used as ceRNA, and targeted inhibition of chi-miR-423-5p on PDGFA mRNA is effectively relieved through competitive combination of chi-miR-423-5p, so that proliferation of mammary epithelial cells is promoted, and apoptosis is inhibited. The research results of the invention not only fill the blank of research on the regulation and control mechanism of the breast epithelial cell ceRNA network of the milk goat, but also provide a theoretical basis for breast development regulation and control, tissue repair and prevention and treatment of related diseases, and lay an important foundation for developing a potential molecular intervention strategy.