52 results about "Transcriptome profiling" patented technology

The invention discloses an ornithogalum thyrsoides QtHIPP37 gene and application thereof. The nucleotide sequence of the gene is as shown in SEQ ID NO.1, and the amino acid sequence coded by the geneis as shown in SEQ ID NO.2. According to the ornithogalum thyrsoides QtHIPP37 gene and application thereof, on the basis of establishing a high-efficiency regeneration system and transcriptome analysis of a bulbil on leaves of ornithogalum thyrsoides, the QtHIPP37 gene is cloned and an over-expression vector is constructed, the QtHIPP37 gene and the over-expression vector are introduced into modelplant tobacco, the stress resistance of the transgenic tobacco to the drought stress is remarkably improved, and therefore it is proved that the QtHIPP37 gene can improve the stress resistance performance such as the drought resistance and the saline-alkali resistance of plants from the molecular level and has a good application prospect in plant biotechnology application.

Synthetic hydrogels for organogenesis support organogenesis from mammalian cells, including human cells. The synthetic hydrogels typically include a network of crosslinked branched biodegradable polymers. A portion of the branches of the branched biodegradable polymers are linked to binders which are generally synthetic peptides for cell and extracellular matrix attachment. The hydrogels may include an inhibitor of apoptosis. The synthetic hydrogels with the synthetic binders typically do not interfere with cellular, proteomic, genetic, and/or transcriptome analyses of organoids formed in the hydrogel. The synthetic hydrogels may be subject to on-demand dissolution to provide intact organoids substantially free of hydrogel polymers. Also provided are methods of making the synthetic hydrogels and methods of using the synthetic hydrogels for organogenesis.

A novel transcriptome analyzing method and to provide a gene found by this method and a protein encoded by the gene. A method for determining whether or not a continued arbitrary DNA sequence existing in the genome of an arbitrary biological species, in which the nucleotide sequence is already known but its possibility of being a gene expression region is unclear (specific region), is the specific region, which comprises detecting whether or not a nucleotide sequence that corresponds to the nucleotide sequence of the region is present in the RNA of the biological species, and a method for determining the gene expression region in an arbitrary region on a genome or the entire genome, which comprises repeatedly carrying out the above method.

Provided herein are methods for target gene sequencing and single cell barcoding in conjunction with analysis of gene expression in single cells. In some embodiments, the target gene is an immune molecule, such as an antibody or TCR. In some embodiments, the methods can be used to carry out transcriptome sequencing, e.g., RNA sequencing, to capture transcriptome of single cells paired with full receptor immune receptor sequences such that information about the immune repertoire and transcriptome of a cell can be determined. Also provided are polynucleotide libraries for use in carrying out transcriptome analysis and immune molecule, e.g., antibody or TCR, sequencing.

The invention provides a transcriptome analysis method and system without a reference genome sequence. The analysis method comprises the following steps: acquiring second-generation RNA effective sequencing data and third-generation RNA effective sequencing data of a to-be-detected sample; correcting the third-generation RNA effective sequencing data by utilizing the second-generation RNA effective sequencing data; redundancy elimination is carried out on the valid data after the third-generation correction to obtain a unigene sequence; performing sequence comparison on the second-generation RNA effective sequencing data and the unigene sequences, and performing statistics on the reads number on each unigene sequence by utilizing a comparison file to obtain an expression level FPKM value of each gene. The analysis method integrates the advantages of a second-generation sequencing technology and a third-generation sequencing technology, and solves the problem that no transcriptome of areference-free genome sequence is analyzed by utilizing third-generation sequencing data at present.

An embodiment of the invention provides an analysis method for multi-sample-size comparative transcriptomes based on third-generation sequencing detection. The method comprises the following steps: carrying out quality control on data obtained after third-generation sequencing, acquiring a third-generation full-length transcript, carrying out CDS and PEP prediction, carrying out gene family clustering based on prediction results, and acquiring orthologous genes, paralogous genes and species-specific genes; carrying out macroscopic evolution analysis, SSR detection and marker development on theorthologous genes, carrying out functional gene localization, and excavating tachytelic evolution genes of different subspecies or near-source species of a researched material; carrying out WGD eventdetection and gene family tree analysis of individual families on the paralogous genes; and subjecting the species-specific genes to database annotation to clearly learn about the specific functionsof the specific genes of the researched material. The embodiment of the invention provides a set of perfect scientific research method for bioinformatics research on the whole so as to realize processing of multi-sample-size comparative transcriptome data.

The present invention provides a novel method for the classification of adjuvants. In one embodiment, the present invention provides a method for generating organ transcriptome profiles for adjuvants, said method comprising: (A) a step for obtaining expression data by performing transcriptome analysis for at least one organ of a target organism by using at least two adjuvants; (B) a step for clustering the adjuvants with respect to the expression data; and (C) a step for generating the organ transcriptome profile for the adjuvants on the basis of the clustering.

The invention belongs to the technical field of high-throughput sequencing data analysis, and particularly relates to a method for screening transcription factors related to postharvest softening of grape fruits. According to the invention, hypotaurine (HT) and hydrogen peroxide (H2O2) treatment is carried out on harvested 'Kyoho' grapes, through transcriptome sequencing and weighted gene co-expression network analysis (WGCNA), correlation analysis is carried out on differential expression genes obtained through transcriptome analysis and pectin content change, a differential expression gene module closely related to the pectin content change is screened out, and the specific value of the differential expression genes and the specific value of the pectin content change are obtained. And excavating differential expression transcription factors in the softening process of the picked grape fruits. According to the method, the softening character related transcription factors can be effectively screened, and a theoretical reference is provided for researching the softening occurrence mechanism of the picked grape fruits.

The invention relates to the technical field of biology, and particularly relates to a comparative transcriptome analysis method for peanut leaf gene differential expression under intercropping corn. The method comprises the steps that an RNA-seq technology is utilized for comparing and analyzing differential expression genes of peanut functional leaves in the pod expansion period under peanut single cropping and intercropping corn stress; differential genes related to metabolic pathways are taken as main genes, important genes and key metabolic pathways formed by peanut pod yield under intercropping corn stress are excavated, and a theoretical basis is provided for reducing adverse effects of intercropping corn stress on peanut yield by means of a directional chemical regulation and control technology; and the relative expression level of candidate differential expression genes is verified through qRT-PCR detection, and finally the qRT-PCR detection result is roughly consistent with multiple changes in transcriptome sequencing analysis. The transcriptome sequencing analysis method is accurate, feasible, effective and simple.

The invention discloses a primer pair for identifying carrot petal cytoplasmic male sterility and application thereof, the primer pair is designed according to an Indel molecular marker screened by transcriptome analysis, and the application is that the primer pair is adopted to identify carrot petal cytoplasmic male sterility. According to the application, transcriptome sequencing analysis is carried out on total RNA (Ribonucleic Acid) of a group of stable carrot petal cytoplasmic male sterile lines and maintainer lines thereof, comparison with a published carrot reference mitochondrial genome is carried out, Indel loci with differences between the sterile lines and the maintainer lines are screened out, and primers are designed. Specific amplification verification is carried out between fertile plants and sterile plants of different varieties of carrots, the result shows that the primer pair can completely distinguish the fertility of the variety to be detected, the carrot variety with cytoplasmic male sterility can be rapidly screened out in the seedling stage, the accuracy rate is high, and the method can be used for removing abnormal plants in the breeding process. The method has important practical application value and market prospect.

Provided herein are compositions, kits and methods for the production of strand-specific cDNA libraries. The compositions, kits and methods utilize properties of double stranded polynucleotides, such as RNA-cDNA duplexes to capture and incorporate a novel sequencing adapter. The methods are useful transcriptome profiling by massive parallel sequence, such as full-length RNA sequencing (RNA-Seq) and 3′ tag digital gene expression (DGE).

Disclosed herein include methods and compositions for selectively amplifying and/or extending nucleic acid target molecules in a sample. The methods and compositions can, for example, reduce the amplification and/or extension of undesirable nucleic acid species in the sample, and/or allow selective removal of undesirable nucleic acid species in the sample.

A fundamental shortcoming in the current treatment of schizophrenia is the lack of valid criteria to predict who will respond to antipsychotic treatment. The identification of blood-based biological markers of the therapeutic response would enable clinicians to identify the subgroup of patients in whom conventional antipsychotic treatment is ineffective and offer alternative treatments. As part of the Optimization of Treatment and Management of Schizophrenia in Europe (OPTiMiSE) programme, the inventors conducted a transcriptome analysis on 188 subjects with first episode psychosis, all of whom were subsequently treated with amisulpride for 4 weeks. They identify 32 genes for which the expression changed after treatment in good responders only. Among these genes, the expression of ALPL, a gene involved in vitamin B6 metabolism, as well as CA4, DGTA2, DHRS13, HOMER3 and WLS showed a significant difference in expression level between good and poor responders before starting treatment, allowing to predict treatment outcome with a predictive value of 93.8% when combined with clinical features Collectively, these findings identified new mechanisms to explain symptom improvement after amisulpride medication and highlight the potential of combining gene-expression profiling with clinical data to predict treatment response in first episode psychoses.

The invention provides a single-celled spatial transcriptome analysis method. Specifically, the invention provides a single-celled spatial transcriptome capable of detecting an undissociated state. According to the method provided by the invention, single cells can be collected in a high flux manner on the basis of reserving spatial position information of cells in tissue, quantified cellular transcriptome data with high sensitivity and high repeatability are obtained through secondary high-flux sequencing, single-celled spatial transcriptome sequencing data of each target cell are mapped to corresponding spaces of a tissue sample based on three-dimensional coordinate values of each target cell, and thus, a single-celled spatial transcriptome sequencing data set of the tissue sample is obtained. The method provided by the invention can be extensively applied to quantitative research on single-celled gene expression of normal and diseased tissue and provides a more efficient and accurate tool for researching states and functions of cells of the tissue.

The invention discloses a third-generation full-length transcriptome analysis method suitable for a Sequel sequencing platform, which is characterized by comprising the following steps: 1, a sequencing data filtering step; 2, a sequencing data comparison step; 3, a transcript annotation step; 4, an ORF prediction step; 5, a transcript function annotation step; 6, a fusion gene analysis step; 7, aLncRNA prediction step; 8, variable shear analysis step; and 9, a variable polyadenylation analysis step. According to the method, the running speed is higher, annotation on the transcript is finer compared with common matchannot software, and the type of the transcript is more convenient to analyze.

The invention belongs to the technical field of biology, and particularly relates to a method for rapidly identifying a gene for regulating and controlling the oil content of rape based on a genomics approach and an application of the method. According to the technical key points, the method comprises the following steps: screening a high-oil-content inbred line 1L99 and a low-oil-content inbred line 1L363 through field multi-year multi-point tests, and then carrying out transcriptome sequencing analysis on seeds of the two inbred lines in six different development stages; differential genes obtained through transcriptome analysis are scanned at a qOC-A5QTL site, and it is found that the expression quantity of the BnECH.A5 gene in different rape seed development stages of a high-oil-content inbred line is low, the expression quantity of the BnECH.A5 gene in a low-oil-content inbred line is high, and the expression quantity of the BnECH.A5 gene in the key stage of seed oil content accumulation within 30-44 days after flowering changes drastically. The mutant plant of the gene is constructed, the result shows that the oil content of a function-deleted mutant plant is remarkably increased compared with that of a wild plant.