29 results about "Ribosomal RNA" patented technology

The invention provides a macro virus group sequencing library construction method for removing host ribosome RNA through an enzyme method and a kit, and belongs to the technical field of biology. The method comprises the following steps: hybridizing total RNA (Ribonucleic Acid) of a sample with a DNA (Deoxyribose Nucleic Acid) probe aiming at host ribosome RNA to form a DNA / RNA hybrid chain; rNase H is used for digesting RNA in the hybrid chain, and DNase I is used for digesting the remaining DNA probe in the system; purifying to obtain virus RNA (Ribonucleic Acid); carrying out fragmentation treatment on the virus RNA; carrying out reverse transcription on the fragmented RNA to synthesize a first chain cDNA, then synthesizing a second chain cDNA, and carrying out terminal repair and dA tail addition to obtain double-chain cDNA; connecting the linker with the dT tail with the double-chain cDNA; and carrying out PCR amplification and purification on the connection product to obtain the macro virus group sequencing library. According to the construction method and the kit, the problem that the full-length sequence of the virus cannot be obtained from a low-load sample can be solved.

The invention provides a method for eliminating ribosomal RNA in a mouse total RNA sample, which comprises the following steps: carrying out reverse transcription on the total RNA in the mouse sample into cDNA, and amplifying the cDNA by adopting a primer sequence group to obtain a DNA fragment covering all sequences of the mouse ribosomal RNA; carrying out amplification by taking the DNA fragment as a template and adopting a single primer in the primer sequence group to obtain a single-stranded DNA probe; hybridizing the total RNA of the mouse sample by adopting a single-stranded DNA probe, and performing RNase H digestion to obtain a digestion product; sequentially carrying out DNase I digestion and RNA purification on the digestion product to obtain a target product; wherein the primer sequence group comprises upstream primers from the first to the nineteenth and downstream primers from the first to the nineteenth, and the primer sequence group has the characteristics of low cost, stable performance and high reduction efficiency.

The application discloses a LAMP primer group, a kit and a detection method for detecting Pinus armandii rust fungus, and belongs to the technical field of genetic engineering. The application takes the specific nucleotide sequence of the large subunit ribosomal RNA of the Pinus armandii rust fungus as a target gene to design and screen a primer group which is specific and high in sensitivity, and can be used for LAMP detection of the Pinus armandii rust fungus. The LAMP primer group provided by the application has the advantages of high universality, high specificity, high sensitivity and good accuracy, and the detection limit can reach 4.5x10 ‑4 ng / μL, which is 100 times higher than the sensitivity of the LAMP detection of different species in the same genus in the prior art, the detection method can rapidly detect the Pinus armandii rust fungus from spore piles and host plant materials, and is suitable for the detection of Pinus armandii seedling materials in forest fields and customs quarantine ports.

The invention discloses an efficient ribosome imprinting sequencing library construction method, and belongs to the technical field of biology. In the enzyme digestion treatment step, a mixed enzyme system of RNase I and micrococcus nuclease is adopted to treat the cell lysis buffer, and the trinucleotide periodicity of RPFs can be remarkably improved to 80% or above. In the target fragment recovery step, the sucrose gradient ultracentrifugation step is omitted, the RPFs are directly recovered by gel electrophoresis, a plurality of enzyme reaction steps in library construction are optimized and integrated, and streptavidin magnetic beads are used for solid phase purification, so that the whole library construction period is greatly shortened from 7 days to 2.5 days. The method does not depend on special equipment such as ultracentrifugation, and can be completed in a conventional molecular biology laboratory. Besides, a multi-enzyme synergistic RNA terminal one-step modification system is innovatively constructed, single-tube one-step completion is realized, the terminal treatment efficiency and consistency are improved, and a key guarantee is provided for obtaining a high-quality and high-complexity Ribo-seq library.

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.

The invention discloses a microbial community identification method and system, and particularly relates to the technical field of microbiomics. A hidden Markov model database constructed on the basis of multiple types of ribosome RNA sequences is adopted for global search, a huge whole genome database in the prior art is replaced, and the size of the database is reduced; moreover, the hypervariable region sequence is extracted from the identified ribosome RNA sequence in a targeted manner, and the extracted sequence data and the quality information in the original sequencing data are pasted back, so that the hypervariable region sequence file containing the complete quality information is generated. The sequence data contains sequence information for identification, and a ribosome RNA marker gene sequence can be accurately identified and extracted from metagenome or metatranscriptome sequencing data; the original sequencing data can be used for a traditional amplicon analysis process, and can also support downstream deep analysis, so that seamless connection with the traditional amplicon analysis process is realized.

The present invention relates to a method for diagnosing lung cancer in a patient by determining the methylation status of a ribosomal RNA (rRNA) fragment.

This invention discloses a compound seed treatment agent containing metalaxyl-M and tebuconazole, its preparation method, and its uses, belonging to the technical field of seed treatment agents. The suspension of this invention uses metalaxyl-M, tebuconazole, and sodium selenite as the main components, supplemented with emulsifying and dispersing agents, wetting and dispersing agents, antifreeze agents, suspending agents, film-forming agents, and warning colors, and is prepared by adding deionized water to a sufficient volume. Metalaxyl-M targets and inhibits ribosomal RNA polymerase I of oomycete pathogens, while tebuconazole targets and inhibits sterol 14α-demethylase. The two have complementary fungicidal spectra, synergistically controlling maize stalk rot and maize head smut. Sodium selenite, by inhibiting the oxidative stress defense system of pathogenic fungi involving glutathione and thioredoxin, promotes the effects of the two main components and simultaneously remediates selenium-deficient soils. This invention is suitable for the green and efficient control of maize stalk rot and head smut, and also has the function of ecological restoration of selenium-deficient soils.

The application belongs to the technical field of fluorescent probes, and particularly relates to a preparation method and application of an RNA fluorescent probe based on biological orthogonal reaction, and the structural formula of the fluorescent probe is: the application provides a preparation method for generating an RNA activated near-infrared fluorescent probe based on biological orthogonal reaction. First, (E)-2-chloro-3-(hydroxymethyl)cyclohex-1-en-1-methanal and 6-bromo-1-ethyl-2-methylquinolin-1-ium salt are used as raw materials to synthesize a precursor compound beta-Br, and then the beta-Br is rapidly in-situ generated into a fluorescent probe under physiological conditions. After the fluorescent probe generated based on biological orthogonal reaction is reacted with RNA, the fluorescence intensity at the near-infrared region 670-900 nm is enhanced with the increase of the RNA concentration, and the fluorescence enhancement multiple reaches 400. Secondly, the fluorescent probe generated based on biological orthogonal reaction shows high selectivity to RNA, and is not affected by other various ions, active oxygen, RNA bases, biological thiols and amino acids. Finally, the fluorescent probe can be washed-free and fast imaging in living cells, and can be in-situ fast generated into a fluorescent probe in cells, and can be used for monitoring intracellular ribosomal RNA, distinguishing between living cells and dead cells, and real-time monitoring of intracellular oxidative stress.

This disclosure provides methods and compositions to increase the efficiency of targeted coding RNA pseudouridylation by H / ACA snoRNA, by localizing the H / ACA snoRNA more to the nucleoplasm where pre-mRNAs are transcribed and processed into mature mRNAs versus the nucleolus, where H / ACA snoRNAs natively modify ribosomal RNAs.

The invention discloses a method and a device for mining virus small interfering RNA (Ribonucleic Acid) through multiple algorithms, and relates to the field of biological detection.The method comprises the following steps: removing linkers of input sequences through multiple linker removing algorithms, and merging and de-duplicating the obtained sequences to obtain linker-removed sequences; mapping the delinker sequence to a ribosome RNA database in a cascade mode through a plurality of mapping algorithms, and outputting a first incompletely mapped sequence; mapping the first incompletely-mapped sequence to a host genome by adopting a same mapping method, and outputting a second incompletely-mapped sequence; and mapping the second incompletely-mapped sequence to the viral genome through a plurality of mapping algorithms, and judging that the second incompletely-mapped sequence is from the viral sequence when the second incompletely-mapped sequence is mapped to the viral genome by any mapping algorithm in a way that the mismatched base number is less than or equal to 1. According to the method, the efficiency and the accuracy of mining the virus small interfering RNA from massive transcriptome data are remarkably improved.

The application belongs to the technical field of microorganism detection, and particularly relates to detection primers and probes for Euryphallus sinensis and application thereof. The application establishes a real-time fluorescent quantitative PCR method for the pathogen based on TaqMan-MGB probes according to the small subunit ribosomal RNA (SSUrRNA) gene of Euryphallus sinensis, and designs detection primers based on isothermal amplification technology. With the constructed recombinant plasmid standard as a template, the detection sensitivity of the quantitative PCR detection method for the target gene is 9.58 copies / reaction. The detection primers for isothermal amplification can be detected under simple constant temperature conditions, and the color change of the detection product after adding nucleic acid dye can realize on-site rapid diagnosis of the pathogen.

The invention provides a method for eliminating ribosomal RNA in a bovine total RNA sample, which comprises the following steps: reversely transcribing the total RNA in the bovine sample into cDNA, and amplifying the cDNA by using a primer sequence group to obtain a DNA fragment covering all sequences of the bovine ribosomal RNA; carrying out amplification by taking the DNA fragment as a template and adopting a single primer in the primer sequence group to obtain a single-stranded DNA probe; hybridizing the total RNA of the cattle sample by adopting a single-stranded DNA probe, and performing RNase H digestion to obtain a digestion product; sequentially carrying out DNase I digestion and RNA purification on the digestion product to obtain a target product; wherein the primer sequence group comprises first to seventeenth upstream primers and first to seventeenth downstream primers, and the primer sequence group has the characteristics of low cost, stable performance and high reduction efficiency.

Provided are methods of producing a nucleic acid complex. In certain aspects, the methods include combining a sample including ribosomal RNA (rRNA) and a probe complement oligonucleotide with an oligonucleotide probe. The oligonucleotide probe includes a 3′ region complementary to a 3′ region of a rRNA, and a 5′ region complementary to the probe complement oligonucleotide. The combining is under conditions in which the 3′ region of the oligonucleotide probe hybridizes to the 3′ region of the rRNA and the 5′ region of the oligonucleotide probe hybridizes to the probe complement oligonucleotide, thereby producing a nucleic acid complex. In certain aspects, the methods find use in producing rRNA libraries that find use, e.g., in rRNA sequencing applications. Oligonucleotide probes, libraries thereof, compositions, and kits that find use, e.g., in practicing the methods of the present disclosure, are also provided.

The invention provides a dual-nucleic acid library co-construction method for synchronous detection of plasma ecDNA and related RNA markers. The method comprises the following steps: firstly, extracting total free nucleic acid from the same plasma sample; then carrying out linear DNA digestion treatment; then removing ribosome RNA (Ribose Nucleic Acid); then carrying out reverse transcription reaction by using a chimeric primer with 6-9 random basic groups at the 3'end and a template conversion oligonucleotide sequence at the 5 'end to obtain single-stranded cDNA with universal joints at the two ends; next, the single-stranded cDNA is subjected to cyclization, and annular cDNA is formed; then carrying out rolling circle amplification on the ecDNA and the annular cDNA; and carrying out fragmentation, terminal repair, linker connection and PCR enrichment on the amplification product to obtain the dual-nucleic acid library for high-throughput sequencing. By adopting the method, the collaborative analysis of the DNA level and the RNA level of the trace sample is realized.

The application provides a method for constructing a high-throughput sequencing library of lncRNA and application. The method for constructing the high-throughput sequencing library of lncRNA comprises the following steps: S1, removing ribosomal RNA in total RNA of a sample to be detected to obtain total RNA without ribosomal RNA; S2, reverse transcribing the total RNA without ribosomal RNA to form double-stranded cDNA; S3, connecting sequencing adapters to the 5' and 3' ends of the double-stranded cDNA to obtain an adapter connection product; S4, PCR amplification and enrichment of the adapter connection product, and recovery to obtain a high-throughput sequencing library of lncRNA of the sample to be detected; the sample to be detected comprises an exosome sample or a low-quality FFPR sample. The method can solve the problem that unknown lncRNA is difficult to be subjected to high-throughput sequencing in the prior art and is suitable for the field of life science technology.

Provided herein are methods, compositions, and systems for processing nucleic acids from individual cells or cell populations. Cells are co-partitioned and processed, allowing for analysis of a variety of types of RNA from cells while minimizing ribosomal RNA species. The present invention enables high-throughput measurement of full length RNA from single cells with a streamlined workflow.

The invention provides a method for eliminating ribosomal RNA in a human total RNA sample, which comprises the following steps: carrying out reverse transcription on the total RNA in a human blood sample into cDNA, and amplifying the cDNA by adopting a primer sequence group to obtain a DNA fragment covering all sequences of the human ribosomal RNA; carrying out amplification by taking the DNA fragment as a template and adopting a single primer in the primer sequence group to obtain a single-stranded DNA probe; hybridizing the total RNA of the human blood sample by adopting a single-stranded DNA probe, and performing RNase H digestion to obtain a digestion product; sequentially carrying out DNase I digestion and RNA purification on the digestion product to obtain a target product; wherein the primer sequence group comprises upstream primers from the first to the nineteenth and downstream primers from the first to the nineteenth, and the primer sequence group has the characteristics of low cost, stable performance and high reduction efficiency.

The present invention relates to a 28S ribosomal RNA (rRNA) region binding molecule for use in medicine, preferably for use in the treatment of lung cancer.

The invention provides a method for eliminating ribosome RNA (Ribosome Ribonucleic Acid) in a pig total RNA (Ribosome Ribonucleic Acid) sample, which comprises the following steps: reversely transcribing the total RNA in the pig sample into cDNA (Complementary Deoxyribonucleic Acid), and amplifying the cDNA by adopting a primer sequence group to obtain a DNA fragment covering all sequences of the pig ribosome RNA; carrying out amplification by taking the DNA fragment as a template and adopting a single primer in the primer sequence group to obtain a single-stranded DNA probe; hybridizing the total RNA of the pig sample by adopting a single-stranded DNA probe, and performing RNase H digestion to obtain a digestion product; sequentially carrying out DNase I digestion and RNA purification on the digestion product to obtain a target product; wherein the primer sequence group comprises first to fifteenth upstream primers and first to fifteenth downstream primers, and the primer sequence group has the characteristics of low cost, stable performance and high reduction efficiency.

A method for identifying exogenous viruses based on metagenomic sequencing, comprising the following steps: S1, a data quality control step, filtering the quality of the metagenomic sequencing raw data of the sample to obtain clean sequencing data; S2, a host removal step, aligning the clean sequencing data with a host reference genome and a ribosomal RNA database, removing the host sequences on the alignment, and obtaining enriched microbial sequences. The method integrates kraken2 species identification, RVDB / nt_core database alignment, virsorter2 / checkV verification and other multiple links to form a multi-dimensional identification system, improve the accuracy and reliability of virus identification, introduce a multi-process parallel processing mechanism to support the synchronous analysis of batch samples, greatly improve the analysis efficiency, adapt to the high-throughput detection needs of large-scale cell banks, biological products intermediates and finished products, and solve the problem of low throughput of traditional methods and existing mNGS methods.

In an example of a method, a primer functionalized, ribosomal RNA (rRNA) depleted sample is generated. The primer functionalized, rRNA depleted sample is combined with a composition to form a mixture, where the composition includes a reverse transcriptase, an RNA nickase, a DNA polymerase with strand displacement activity or 5'-3' exonuclease activity, and a plurality of deoxynucleotide trisphosphates. The mixture is introduced into a flow cell including a substrate, first and second primers immobilized on the substrate, and first and second transposome complexes immobilized on the substrate. A temperature protocol is initiated to form double-stranded complementary DNA (cDNA) from the primer functionalized, rRNA depleted sample and to form partially adapted cDNA fragments from the double-stranded cDNA.

The application discloses OsRNE A gene and application of the gene and a coded protein in rice leaf color regulation and chloroplast development. OsRNE The nucleotide sequence of the gene is shown as SEQ ID NO. 1, and the amino acid sequence of the coded protein is shown as SEQ ID NO. 2. OsRNE The application utilizes CRISPR / Cas9 gene editing technology to knockout the gene and obtain a loss-of-function mutant. The mutation of the gene leads to impaired chloroplast development of rice, affects chlorophyll synthesis, albino of seedlings and death within three-leaf stage, and thus can be used as a marker trait to assist rice molecular breeding at the seedling stage. OsRNE The gene is mainly expressed in leaves, the coded protein is located in chloroplasts, and the chloroplast development and normal growth of seedlings are affected by affecting the metabolism of ribosomal RNA in chloroplasts. Therefore, the application can be applied to molecular genetic breeding of rice leaf color traits, and has important significance for further understanding of a chloroplast development regulation mechanism of rice and yield increase of rice.

This invention discloses a method and apparatus for mining viral micro-interference RNA using multiple algorithms, relating to the field of biological detection. The method includes: removing adapters from an input sequence using multiple adapter removal algorithms, merging and deduplicating the resulting sequences to obtain an adapter-removed sequence; mapping the adapter-removed sequence to a ribosomal RNA database using multiple mapping algorithms in a cascaded manner, outputting a first incompletely mapped sequence; mapping the first incompletely mapped sequence to a host genome using the same mapping method, outputting a second incompletely mapped sequence; mapping the second incompletely mapped sequence to a viral genome using multiple mapping algorithms. If the second incompletely mapped sequence is mapped to the viral genome by any mapping algorithm with a mismatch number ≤ 1, it is determined to originate from a viral sequence. This invention significantly improves the efficiency and accuracy of mining viral micro-interference RNA from massive transcriptome data.

This disclosure provides methods and compositions to increase the efficiency of targeted coding RNA pseudouridylation by H / ACA snoRNA, by localizing the H / ACA snoRNA more to the nucleoplasm where pre-mRNAs are transcribed and processed into mature mRNAs versus the nucleolus, where H / ACA snoRNAs natively modify ribosomal RNAs.

This invention proposes a spatial whole-transcriptional sequencing method and application suitable for tobacco petiole tissue. The method employs tissue embedding and frozen sectioning techniques suitable for tobacco petioles, effectively ensuring uniform and flat sections and maintaining structural integrity. A pretreatment solution suitable for plant tissue permeation effectively enzymatically dissolves plant cell walls and increases cell membrane permeability, facilitating better RNA release. An in-situ polyadenylation treatment method suitable for tobacco petiole tissue effectively polyadenylates non-coding RNA in the sectioned samples, improving non-coding RNA capture efficiency. A method suitable for spatial whole-transcriptional sequencing workflows to remove rRNA from cDNA libraries effectively removes rRNA from the library through wet experimental ends, avoiding reduced sequencing depth for other RNA types due to excessive ribosomal RNA capture, thus greatly improving data utilization. This invention has broad application prospects.

Described herein is a database of probe sequences and a set of probes that enable the detection, identification and differentiation of bacteria, and one or more of 16S ribosomal RNA pathogenicity elements, and / or antimicrobial resistance (AMR) genes. These sequences or probes have many uses including but not limited to use in a sequence capture platform and other diagnostic assays. The sequences or probes described herein increase the sensitivity of high-throughput sequencing for detection, identification, and differentiation of bacteria, and one or more of 16S ribosomal RNA, pathogenicity elements, and AMR genes.

The invention provides a method for eliminating ribosomal RNA in a chicken total RNA sample, which comprises the following steps: carrying out reverse transcription on the total RNA in the chicken sample to obtain cDNA, and amplifying the cDNA by adopting a primer sequence group to obtain a DNA fragment covering all sequences of the chicken ribosomal RNA; carrying out amplification by taking the DNA fragment as a template and adopting a single primer in the primer sequence group to obtain a single-stranded DNA probe; hybridizing the total RNA of the chicken sample by adopting a single-stranded DNA probe, and performing RNase H digestion to obtain a digestion product; sequentially carrying out DNase I digestion and RNA purification on the digestion product to obtain a target product; wherein the primer sequence group comprises first to seventeenth upstream primers and first to seventeenth downstream primers, and the primer sequence group has the characteristics of low cost, stable performance and high reduction efficiency.

This invention discloses a method and system for identifying microbial communities, particularly relating to the field of microbiome technology. By employing a Hidden Markov Model database constructed based on multiple types of ribosomal RNA sequences for global searching, it replaces the massive whole-genome databases of existing technologies, reducing database size. Furthermore, this invention generates a hypervariable region sequence file containing complete quality information by targeting and extracting hypervariable regions from the identified ribosomal RNA sequences and then back-linking the extracted sequence data with the quality information from the original sequencing data. The sequence data contains sequence information for identification, enabling accurate identification and extraction of ribosomal RNA marker gene sequences from metagenomic or metatranscriptomical sequencing data. The original sequencing data can be used for traditional amplicon analysis workflows and also supports downstream in-depth analysis, achieving seamless integration with traditional amplicon analysis workflows.