44 results about "Transcriptome profiling" patented technology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The invention discloses an SNP molecular marker based on a WAS gene and related to pig hypoxia resistance and application of the SNP molecular marker, the SNP molecular marker is located at the 1756th site of a nucleotide sequence of a WAS gene core promoter region, the basic group is A or T, and under the hypoxia condition, A is a dominant allele; and the nucleotide sequence of the core promoter region of the WAS gene is-1693bp to-2000bp of the sequence as shown in SEQ ID NO. 15. Through high and low altitude transcriptome analysis of Tibetan pigs and a pig skeletal muscle satellite cell hypoxia model, it is found that the WAS gene plays an important role in pig hypoxia resistance, and a WAS gene promoter region is utilized to construct a dual-fluorescein reporter vector to determine an SNP site (g.-1756 Agt; T) affecting pig hypoxia resistance. 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 is a method of single cell transcriptome analysis. The method comprises detecting multiple transcripts in each individual cell of the plurality of cells by barcoding the transcripts with a cell-specific compound barcode formed using a DNA polymerase and a terminal transferase, optionally in a single enzyme such as a reverse transcriptase.

This invention belongs to the fields of molecular genetics and genetic engineering, and discloses a peanut plant type regulating gene, AhERECT1, its mutants, and their applications. The nucleotide sequence of the peanut plant type regulating gene AhERECT1 is shown in SEQ ID NO.1. Its mutant is caused by a single amino acid deletion due to the deletion of nucleotides 38-40 (CTC) in the open reading frame of the gene shown in SEQ ID NO.1, and its nucleotide sequence is shown in SEQ ID NO.2. This invention obtained the AhERECT1 gene through linkage mapping, fine mapping, and transcriptome analysis. Using CRISPR / Cas9 gene editing technology, the erect peanut variety Yuhua 9326 was successfully modified into a semi-vine type through targeted editing. The gene and its mutants of this invention provide key gene resources and efficient technical support for the precise improvement of peanut plant type, and can be widely applied to the breeding of peanut varieties with different plant types, which is of great significance for improving peanut yield and quality.

This invention discloses the chitin synthase 1 (LmCHS1) gene of the leafminer moth, its dsRNA, its synthesis method, and its insect-resistant applications. Through transcriptome analysis, specific primer pairs for the open reading frame of the LmCHS1 gene were designed and synthesized. The LmCHS1 gene sequence was obtained through gene cloning (nucleotide sequence: SEQ ID NO: 1, amino acid sequence: SEQ ID NO: 2). The gene fragment with sequence SEQ ID NO: 3 was selected as the RNAi target sequence. Primer pairs SEQ ID NO: 6 and SEQ ID NO: 7 with restriction enzyme sites were designed and synthesized. PCR amplification was performed, and a prokaryotic expression vector was constructed to induce dsRNA expression. Feeding leafminer moth larvae with dsRNA interfered with LmCHS1 gene expression. After 24 hours, abnormalities were observed in the larvae's body surface, with some larvae failing to complete molting or dying due to an inability to form a normal body surface after molting. After 96 hours, the larval mortality rate was 72.22%, compared to 40% in the GFP control group, demonstrating a significant effect. This invention has broad application prospects in the control of the leaf borer pest in forestry due to its high efficiency, specificity, and safety.

The present disclosure relates to measuring gene expression of cells of a blood sample obtained from a mammalian subject suspected of having a tick-borne disease. In particular, the present disclosure provides tools for determining whether a human subject has acute Lyme disease by transcriptome profiling a peripheral blood mononuclear cell or a whole blood sample from the subject.

The method of generating multipotent stem cells is a method for producing and / or expanding multipotent stem cells by delivering at least one reprogramming protein into somatic cells. The at least one reprogramming protein includes a Master Regulator (MR) protein, which may be BAZ2B, ZBTB20, ZMAT1, CNOT8, KLF12, DMTF1, HBP1, or FLI1. The bromodomain protein BAZ2B, in particular, was identified by first generating bi-species heterokaryons by fusing Tcf7l1− / − murine embryonic stem cells (ESCs) with human B-cell lymphocytes. Reprogramming of the B-cell nuclei to a multipotent state was tracked by human mRNA transcript profiling at multiple timepoints. Interrogation of a human B-cell regulatory network with gene expression signatures collected from such reprogramming time series identified eight candidate Master Regulator proteins, which were validated in human cord blood-derived hematopoietic progenitor and lineage-committed cells.

The invention relates to the field of plant molecular biotechnology and genetic engineering, and provides a kiwi fruit AcRBCS1 gene, the nucleotide sequence of which is as shown in SEQ ID NO. 1. The invention also provides an editing vector of the gene and a yellowing kiwi fruit mutant. Meanwhile, the invention further provides application of the gene, the editing vector and the yellowed kiwi fruit mutant. The AcRBCS1 gene has the advantages that the AcRBCS1 gene is excavated and clarified through transcriptome analysis, it is proved that the AcRBCS1 gene is a key functional gene for regulating and controlling development and color generation characters of kiwifruit chloroplast, and a yellowing kiwifruit mutant with stable phenotype is successfully obtained; a core gene and a practical material are provided for kiwi fruit color generation mechanism research, rapid green removal germplasm innovation and high-quality new variety breeding.

The present invention relates to the technical field of spatial transcriptomics, and in particular to a method for identifying a cell boundary applied in spatial transcriptomic analysis. In general, during spatial transcriptomic analysis, the procedure substantially comprises sample preparation, optical structure image generation, spatial transcriptomic information collection, alignment of optical structure images with spatial transcriptomic information, and single-cell annotation. The characteristic of the present invention lies in selecting a specific fluorescent protein transgenic animal model and employing an optical and transcriptional image alignment method compatible with the animal model, thereby enabling clear visualization of the structure and contour of a single cell in a sample under a fluorescence imaging system without requiring cell membrane or nuclear staining to obtain a fluorescence image. Consequently, drawbacks of dye‑induced effects on mRNA capture efficiency and sample displacement are avoided. In addition to significantly improving the efficiency of cell boundary identification, the method further enhances the accuracy of subsequent algorithm‑assisted cell image segmentation and large‑language‑model‑assisted cell annotation.

Provided herein are methods and compositions for analysis of a transcriptome, for example detection of a RNA isoform, of a cell, tissue, organ, or subject.

The application discloses a construction method of a human adenovirus type 4 protein V knockout mutant strain and application thereof, and belongs to the technical field of biotechnology. The application precisely knocks out a protein V coding sequence in a human adenovirus type 4 full-genome infectious clone by means of a Red / ET homologous recombination system combined with a ccdB reverse screening technology, and obtains a recombination plasmid pBR322-Ad4-△V-EGFP which is clear in genetic background and highly homozygous in sequence. After the plasmid is transfected into HEK-293 cells, the human adenovirus type 4 protein V knockout mutant strain obtained exhibits a typical “replication-deficient” phenotype: although a particle containing a viral genome can be packaged, the physical titer (4.76×10 6 copies / μL) of the particle is about one order of magnitude lower than that of a wild type, and the progeny virus completely loses secondary infection ability. Transcriptome analysis reveals that the deletion mutation can specifically down-regulate a host proteasome pathway and activate a natural immune response. The mutant strain is high in safety and strong in immunogenicity, and can be used as an ideal attenuated vaccine carrier or a gene therapy tool.

The invention discloses a metabolome and transcriptome analysis method and application in the aspect of traditional Chinese medicine eye masks.The metabolome and transcriptome analysis method comprises the following steps that S1, experimental grouping is conducted, and experimental animals are divided into a control group, a model group and a treatment group according to the standard; s2, after the experiment is finished, collecting a sample for detection; s3, metabonomics analysis is carried out, and specific metabolites related to treatment are screened out; s4, carrying out transcriptomics analysis, and screening out specific genes related to treatment; and S5, according to an analysis result, optimizing drug components so as to regulate and control the metabolic pathway and the gene in a targeted manner. A research method is provided for a treatment scheme of the xerophthalmia, the traditional Chinese medicine eye pad is further applied and developed, the xerophthalmia is treated more accurately, immunity is adjusted, metabolism is balanced, safety is high, and no chemical medicine side effect exists.