231 results about "Transcriptome Sequencing" patented technology

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 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 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 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 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 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 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.

The invention discloses application of a downstream transcription factor ONAC131 of an SL signal channel in improving the antiviral property of rice, and belongs to the technical field of biology. Experiments such as transcriptome sequencing screening, yeast two-hybridization and bimolecular fluorescence complementation verify that ONAC131 is an SL downstream response factor and can interact with MID1 to jointly regulate and control expression of RDR1 and RDR6 and activate an antiviral RNAi pathway. Overexpression of ONAC131 can enhance the resistance of rice to grass stunt virus (RGSV), and otherwise, deletion of ONAC131 can weaken the antiviral effect of rice. The gene supplements an SL downstream regulation framework, provides a new target for rice antiviral molecular breeding, and assists in breeding of new varieties of high-yield and high-resistance rice.

The application provides an analysis method, device and equipment based on single-cell transcriptome sequencing data, which comprises the following steps: performing quality control, downstream analysis and visual display on single-cell transcriptome sequencing expression quantitative data, performing cell filtering by using Grubbs test method to obtain effective single-cell transcriptome sequencing quantitative data, performing initialization clustering analysis on the data to obtain single-cell subgroup classification results; performing screening on the single-cell subgroup classification results to obtain target single-cell subgroups, and performing re-clustering analysis to obtain single-cell sub-subgroup classification results; performing significant difference gene screening analysis on the single-cell transcriptome sequencing quantitative data between single-cell subgroups; and performing regression analysis based on characteristic genes of cell cycles to predict cell division periods corresponding to different cell types. The application effectively solves the technical complex problems of existing single-cell transcriptome sequencing quantitative data analysis, makes data analysis more simple and reliable, and reduces the difficulty of data analysis.

This invention provides a method for identifying abamectin resistance genes in the fall armyworm, dsRNA, and their applications, belonging to the field of molecular biology. This invention combines genome resequencing and transcriptome sequencing to identify key abamectin resistance genes in the fall armyworm. Based on the conserved mRNA sequences of the key resistance genes GSTD6 and CTP6A18, dsRNA was designed, and RNAi technology can effectively reduce the fall armyworm's resistance to abamectin. This has significant practical implications for developing effective fall armyworm resistance management strategies to delay the emergence of resistance and for identifying new targets for pest control.

The application belongs to the technical field of medical biological detection, and particularly relates to a construction method of a cancer drug efficacy prediction model, a molecular marker for evaluating the prognosis of intrahepatic cholangiocarcinoma obtained by the construction method, and application of the molecular marker in preparation of a reagent or kit for evaluating the prognosis of intrahepatic cholangiocarcinoma. The application provides a construction method of a cancer drug efficacy prediction model, and uses the construction method to evaluate the drug efficacy prediction of intrahepatic cholangiocarcinoma. The method can analyze the cell and transcriptome characteristic differences in the tumor environment of different efficacy patients in a high-throughput and high-resolution manner by capturing and transcriptome sequencing of a large number of cells in the tumor environment of different patients, so as to establish the correlation between the proportion of specific cell subgroups in the tumor before treatment and the efficacy of the patient.

The application discloses a kind of screening methods and application of pivot gene related to sheep muscle fatty acid content, to solve the technical problems that local sheep breed sample quantity is limited, traditional single gene analysis method is difficult to analyze fatty acid metabolism regulation from network level.This application carries out transcriptome sequencing to multiple months of muscle tissue of Gangba sheep, constructs gene expression matrix, using weighted gene co-expression network analysis (WGCNA) Combined with module characteristic gene and fatty acid phenotype correlation screening strategy, the pivot gene significantly positively correlated with muscle fatty acid content is obtained.The screening method can construct a robust co-expression network under limited sample size, systematically identify the functional module and core gene related to the content of fatty acids such as linoleic acid, and reveal the dynamics of fatty acid metabolism at different ages, and the method can be extended to other plateau livestock;The screened pivot gene can be used as a molecular breeding marker for early selection of Gangba sheep, and the breeding cycle is shortened.

The application 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; through yield character investigation on 245 upland cotton varieties, GWAS and eQTL positioning are carried out in combination with population genome resequencing and ovule transcriptome sequencing one day after flowering, and a site gene GhNF-YB3 significantly related to cotton yield character is obtained. The gene expression of the gene GhNF-YB3 is significantly positively correlated with two yield characters of seed index and boll weight, and the gene may be a causal gene for regulating cotton seed index character. The nuclear factor YB subunit gene GhNF-YB3 of the application can be applied to identification of high-yield upland cotton varieties and improvement of cotton yield character.

The invention discloses a screening method of a biomarker for auxiliary diagnosis of small cell lung cancer, and relates to the technical field of biomedicine. The method comprises: acquiring multiple groups of samples; the plurality of groups of samples comprise exosome RNA transcriptome sequencing data of a plurality of SCLC patients and a plurality of healthy controls; each piece of exosome RNA transcriptome sequencing data comprises a plurality of RNA characteristics; carrying out technical quality filtering on RNA characteristics in all exosome RNA transcriptome sequencing data, carrying out differential expression analysis on the filtered characteristics, and determining candidate RNA sets of the SCLC patient and the healthy contrast; performing feature selection on the candidate RNA set through three complementary feature selection modes, and screening an optimal exosome RNA marker combination from different quantities of RNA feature combinations through 20 times of iteration and 10-fold nested cross validation; and the optimal exosome RNA marker combination comprises LINC00989, CXCL5, MAP3K7CL and TUBB1 (Tumor Umbrella Blanket B1). The optimal exosome RNA marker combination screened by the method is beneficial to diagnosis of small cell lung cancer.

This invention discloses a single-cell spatial annotation method that integrates image and sequencing data. It obtains candidate cue point locations, cell nucleus instance segmentation masks, and cell nucleus type probability vectors by processing full-field H&E stained tissue images. It also obtains a preprocessed spatial transcriptome raw sequencing matrix and corresponding cell type labels by processing the raw spatial transcriptome sequencing matrix. Each capture site and its corresponding integrated data structure are constructed. Based on rigid constraints on the number of cells allocated to each type within each capture site and main type quota constraints, the main type annotation is written. For cells in the intercapture zone, one or more neighboring capture sites with existing annotation results are found. The main type and cell subtype of the intercapture zone cells are inferred through morphological feature similarity calculation, thus obtaining the annotation result. This solves the problem that existing technologies cannot determine the exact type of each cell in ST-sequencing tissue.

The application discloses a perennial ryegrass heat-resistant gene LpHSP70-10, the gene is significantly up-regulated under high-temperature stress, and reaches a peak at 12 hours, and the nucleotide sequence of the gene is shown as SEQ ID NO. 1; the gene LpHSP70-10 is knocked out through a gene editing technology, and a heat-resistant ryegrass variety is cultivated. Based on whole genome association analysis combined with transcriptome sequencing results, the application finds a gene LpHSP70-10 which is sensitive to heat stress. The heat-resistant gene LpHSP70-10 of the ryegrass provided by the application can regulate the expression of heat stress-related genes, and subsequent gene knockout can improve the heat resistance of the ryegrass, which is helpful for cultivating the ryegrass variety suitable for the growth in the relatively hot southern region, and simultaneously reduces the breeding workload, reduces the breeding scale, shortens the breeding period, improves the breeding efficiency, and accelerates the breeding of the heat-resistant ryegrass variety.

Provided are a transcription factor activity inferring method, an apparatus, a storage medium, and a computer device, relating to the field of transcription factor activity inference. Provided is a method for performing transcription factor activity inference for spatial transcriptome sequencing data. The method specifically comprises: combining spatial position information of genes in the spatial transcriptome sequencing data with a single-cell transcription factor activity analysis method to perform transcription factor activity inference on the spatial transcriptome sequencing data. The method can improve the accuracy of performing transcription factor activity inference on the basis of spatial transcriptome sequencing technology.

The invention provides a method for sorting cell units and application thereof. The method for sorting the cell units comprises the following steps: specifically binding a first probe and a second probe with a target nucleic acid sequence, wherein the interval between binding sites of the first probe and binding sites of the second probe does not exceed a preset length; providing an insertion fragment, a skeleton fragment and a ligase, and setting the nucleic acid sequences of the insertion fragment and the skeleton fragment to be that when the first probe and the second probe are specifically combined with a target nucleic acid sequence, the insertion fragment and the skeleton fragment can be connected into a single-chain loop; performing rolling circle replication on the single-chain loop to obtain a long single-chain molecule, the long single-chain molecule comprising a plurality of repetitive units; combining a third probe with the repeating unit, the third probe carrying a detectable signal; and sorting the cellular units based on the detectable signal. According to the method, the target cell group can be efficiently selected, so that high-quality single cell transcriptome sequencing data can be obtained.

The invention provides a larch pine caterpillar resistance gene mining method based on GWAS and multi-omics data, and belongs to the technical field of gene mining. The method comprises the following steps: S1, carrying out insect-resistant phenotype identification on larch individuals, and carrying out variation identification on the larch individuals based on a liquid-phase gene chip sequencing technology; s2, using a mixed linear model to perform correlation analysis by taking a plot position and phenotype observation time as an interaction environment, taking population density at different observation time as a covariable and taking a larch anti-deciduous pine caterpillar index as a phenotype, and identifying a candidate QTL region; and S3, carrying out transcriptome sequencing on resistance extreme individuals, carrying out variation recognition, comparing read segments to the candidate QTL region, and manually analyzing and annotating a gene structure in the QTL region by using IGV. According to the method disclosed by the invention, low-cost variation recognition, environment noise weakening whole genome association analysis and gene structure accurate annotation on complex genome species are realized.

This invention relates to the field of bioengineering technology, and more particularly to a gene for identifying salt tolerance in upland cotton, GhNRX16, and its molecular marker. The CDS sequence of the upland cotton gene GhNRX16 is shown in SEQ ID NO.1 of the sequence listing. This invention uses RNA-seq technology to screen and identify this salt tolerance-related gene in the transcriptome data of upland cotton under salt stress treatment. Furthermore, the GhNRX16 sequence was obtained through gene cloning, and a transient silencing vector based on VIGS (virus-induced gene silencing) technology was successfully constructed. Experiments using VIGS-mediated gene silencing combined with salt stress treatment showed that silencing the GhNRX16 gene significantly reduced the plant's tolerance to salt stress, demonstrating that normal expression of this gene directly contributes to ensuring the plant's salt stress resistance. These results confirm the crucial role of the GhNRX16 gene in regulating cotton salt tolerance, providing important gene resources and theoretical basis for molecular breeding of salt-tolerant cotton.

The invention discloses a gemcitabine drug sensitive marker, a detection kit and application of the gemcitabine drug sensitive marker, the gemcitabine drug sensitive marker is a gemcitabine drug-resistant marker or / and a gemcitabine sensitive marker, and the gemcitabine drug-resistant marker is one or more of ATOH8, DAPK2, BCL2L2, PNPLA2, SHROOM1, FGGY, CPQ, CPO, SLC10A5, ADAMTS15, COL25A1, ASMTL and ENSG00000286264; the sensitive marker is one or more of FAM163A, KREMEN2, VPS37D, GGCT (Growth Growth Computed Tomography), ADSL (Asymmetrical Digital Subscriber Loop), FOXL2 (Focal OXL2), MAST1 (MAST1), DNAAF3 (Deoxyribose Nucleic Acid Amplified The gemcitabine drug sensitive marker is used for predicting the drug effect of gemcitabine. According to the present invention, the expression of the related molecules is detected through the sequencing of the tissue transcriptome of the urothelial carcinoma patient, or through the PCR, the gene chip, the tissue chip, the NanoString technology, the immunohistochemistry and the ELISA method, and the guidance is provided for the drug use of gemcitabine and the precise treatment of bladder cancer.

The present application relates to the technical field of biological genetic engineering, and particularly relates to a kind of identification of plant salt tolerance land cotton gene GhNRX71 And molecular marker, the CDS sequence of the land cotton gene GhNRX71 As shown in SEQ ID NO.1 In the sequence table.The present application is screened and identified in the transcriptome data of land cotton under salt stress treatment by transcriptome sequencing (RNA-seq) technology.The sequence of GhNRX71 Is obtained by further gene cloning means, and the transient silencing vector based on VIGS (virus-induced gene silencing) technology is successfully constructed.The results show that the tolerance of plant to salt stress significantly reduces after silencing GhNRX71 Gene by using VIGS-mediated gene silencing combined with salt stress treatment experiment, which proves that the normal expression of the gene has a direct effect on guaranteeing the salt stress resistance of plant.The above results confirm that GhNRX71 Gene plays a key role in regulating the salt tolerance of cotton, and provides important gene resources and theoretical basis for cotton salt-tolerant molecular breeding.