26 results about "Direct sequencing" patented technology

Provided herein are methods of interrogating spatial gene expression in a sample using substrates having sequencing pores. The disclosed methods allow for spatial analysis of analytes from biological samples using a pore-based sequencing approach and without the need for a barcoded spatial array. In some embodiments, an analyte or intermediate agent thereof, is released from a biological sample and directly sequenced by traversing through pores of a sequencing array including a plurality of pores, e.g., nanopores. In some embodiments, light or other stimuli is used to release an analyte or intermediate agent thereof from a specific region of interest in the biological sample followed by sequencing using sequencing array including a plurality of pores.

The invention relates to the technical field of biology, and discloses a linker element and a method for constructing an oxford nanopore direct RNA sequencing library by the linker element, and the linker element comprises a partial double-strand dump structure formed by annealing a first nucleotide strand S and a second nucleotide strand AS; the first nucleotide chain S sequentially comprises a ligase recognition motif region, a sample tag sequence region, a first universal sequence region and a second universal sequence region in the 5 '-3' direction; the second nucleotide AS sequentially comprises a third universal sequence region, a first universal sequence reverse complementary region, a sample tag sequence reverse complementary region, a ligase recognition motif reverse complementary region and a polyadenylate tail recognition region according to the 5 '-3' direction. According to the method, RNA can be efficiently utilized, the high sequencing data utilization rate and high resolution uniformity are achieved, the technical problems that an existing Oxford nanopore direct RNA sequencing technology cannot effectively utilize initial RNA, and a plurality of library samples cannot be effectively split on the same chip are solved, and the economic and time cost of a practical application end is reduced.

The present invention relates to a single nucleotide polymorphism detection primer for the sheep BMPR1B gene and its application, belonging to the field of gene technology. The SNP molecular marker corresponding to the primer of the present invention is located on chromosome 6 of the BMPR1B gene, and the primer is used for sheep marker-assisted selection breeding. The present invention provides a plurality of SNP molecular marker sites related to sheep reproductive traits, and determines the genotype of each site by directly sequencing the PCR product using sheep blood genomic DNA as a template. The present invention can be used as an effective molecular marker to improve sheep reproductive traits. The detection method is simple, rapid, and highly accurate, which can improve the breeding efficiency of sheep. It has high application value and provides more ways for the screening research of sheep reproductive traits.

The invention belongs to the technical field of Hu sheep molecular marker-assisted breeding, and particularly relates to application of an FABP3 gene molecular marker g.2596A > C in Hu sheep molecular marker-assisted breeding. According to the invention, Hu sheep is taken as a research object, PCR amplification, direct sequencing of products and sequence analysis are adopted, FABP3 gene polymorphism is analyzed, and correlation between different genotypes of polymorphic sites and different growth traits is comprehensively analyzed. An analysis result shows that g.2596A > C is obviously related to the birth weight of Hu sheep, and the birth weight of AA genotype is obviously higher than that of CC genotype (P > 0.05).

This invention provides a simple, rapid, low-cost, high-throughput, and accurate integrated solution that eliminates the need for nucleic acid extraction and purification. It enables targeted capture, amplification, and first-generation sequencing analysis of all key regions of the ABO gene directly from various clinical samples, including whole blood, saliva, oral swabs, and dried blood spots. The operation is simple and low-cost, thus achieving accurate ABO blood typing, subtype analysis, and the discovery of new variants. The method described in this invention can be applied to the identification of difficult blood types, and can discover new ABO alleles, blood group gene chimeras, and rare blood types such as subtype-related intron mutations.

The application discloses a SNP molecular marker of a site rs338618851 related to pork production efficiency of pigs and application. The genetic marker is cloned from a 93991071 site of a chromosome 6 of pigs. American Landrace pigs are selected as test materials, whole genome DNA is extracted from blood of the pigs, and a primer is designed according to a pig genome sequence NC_010448.4 published in an NCBI database. A base substitution of T or C exists at a 172th position of a primer amplification sequence, the substitution causes polymorphism at the position. The SNP site is typed through a direct sequencing technology, and correlation analysis shows that, compared with other gene individuals, a TT genotype individual at the 172th position is large in birth weight, large in eye muscle area and short in time to reach 100 kg at a certain age. The application provides a new marker for molecular breeding of pork production traits of pigs.

Disclosed is a method of training a complete DNA basecaller using high complex direct RNA sequencing (DRS) training datasets and applications of the trained complete DNA basecaller. Including a method to sequence single-cell RNA using capture oligonucleotides and oligonucleotides-DNA barcodes. The training of the DNA basecaller use a linked DNA-RNA oligonucleotide, in which the DNA part is complementary to the RNA part.

The invention provides a digital micro-fluidic chip and an integrated sequencing system and method.The digital micro-fluidic chip comprises a chip body and at least one nucleic acid extraction and library construction unit, and the nucleic acid extraction and library construction unit is arranged in the chip body and comprises a nucleic acid extraction module and a library construction module which are communicated; the nucleic acid extraction process and the library construction process can be continuously completed on the same digital micro-fluidic chip, manual or external intervention is not needed, and the constructed library can be transferred to a sequencer for direct sequencing. The whole process of nucleic acid extraction, library construction and sequencing can be automated, the reagent dosage can be reduced, the library construction and sequencing cost can be reduced, and the library construction and sequencing time can be shortened. The integrated sequencing system disclosed by the invention can realize smaller volume and electricity consumption, needs less manual operation, has low requirements on use environments (such as temperature, humidity, ventilation and the like), can be used in environments outside a laboratory, and is suitable for various application scenes.

The application discloses a SNP molecular marker related to growth traits of Haimen goats and application thereof, and belongs to the field of biotechnology and livestock breeding. The SNP molecular marker comprises an EGFR g.776097C>T mutation site. The application adopts a method of directly sequencing a PCR product as a template of blood genomic DNA of the Haimen goats to determine the genotype. The CC genotype is significantly related to the body length of the Haimen goats at three months old and the body weight, body length, body height, chest depth and chest circumference traits of the Haimen goats at six months old, and can be used as an effective molecular marker for improving the growth traits of the Haimen goats. The detection method is simple, rapid, accurate and low in price, can improve the breeding efficiency of the Haimen goats, and has high application value.

Disclosed are methods of preparing sequencing libraries to quantify tRNA abundance and tRNA modifications in an RNA sample, the methods comprising contacting the RNA with an oligonucleotide in the presence of a ligation agent, and performing nanopore direct sequencing. Also disclosed are kits for performing the methods.

The application belongs to bioengineering technology and particularly relates to a haplotype breeding marker related to pig feed utilization rate and meat production traits and application. The genetic marker is cloned from 19 sites of a SYISL gene promoter of a pig chromosome 8. Three pairs of primers are designed according to a pig genome sequence (NC_010450.4) published by NCBI database. There are 19 base substitutions in the amplified sequences of the three pairs of primers. The SNPs sites are typed by a direct sequencing technology, and the linkage disequilibrium analysis result shows that the 19 sites are all in a complete linkage disequilibrium state, and two haplotypes are generated by analysis. Correlation analysis shows that compared with other haplotype individuals, the H2-H2 combined haplotype individuals have thinner backfat thickness, larger eye muscle thickness, less average feed intake of 30-100 kg body weight and smaller feed-meat ratio. The application provides a new marker for pig meat production trait molecular breeding.

Embodiments of the present application provide a direct RNA sequencing multi-omics analysis method, system, device and storage medium, relating to the technical field of biological information processing. The method comprises: obtaining sequencing data of direct RNA sequencing; aligning the sequencing data with a reference genome to obtain sequencing alignment data; performing full-length transcript identification according to the sequencing alignment data to obtain full-length transcript sequence data; performing transcript quantification processing on the sequencing data based on the full-length transcript sequence data to obtain transcript quantification data; processing the sequencing data according to a methylation modification prediction model to obtain methylation modification data; processing the full-length transcript sequence data according to a nascent mRNA prediction model to obtain nascent mRNA data; and performing correlation analysis according to the full-length transcript sequence data, the transcript quantification data, the methylation modification data and the nascent mRNA data to obtain direct RNA sequencing multi-dimensional information. The method can achieve the technical effect of sequencing accuracy.

The invention discloses a probe set and a kit for specifically enriching RSV whole genome in a respiratory tract sample and application, the probe set provided by the invention can perform high-sensitivity and high-specificity capture and enrichment on RSVA subtype and RSVB subtype free nucleic acid fragments in the respiratory tract sample so as to obtain a high-quality whole genome sequence. Compared with sequencing after purification culture, the method disclosed by the invention can be used for carrying out whole genome sequencing on RSV which is a pathogen difficult to culture, and is wider in application range. Compared with direct sequencing of a positive sample, the method has the advantages that the pathogen detection target is higher, the influence of other sequences is smaller, the interference of impurities can be effectively reduced, the sample pathogen abundance required by high-quality whole genome sequencing can be completed, and the high-quality RSV whole genome sequence acquisition of more samples can be completed.

Disclosed are nucleic acid analysis and sequencing technologies. The disclosure addresses the preparation of transfer RNA (tRNA) constructs suitable for direct RNA sequencing and structural applications by enzymatically ligating multiple tRNA molecules into a single, longer RNA strand using designed RNA oligonucleotides. Disclosed are methods of preparing a sequencing library for a plurality of tRNAs and kits.

Disclosed is a method of pre-processing and inferencing data for RNA chemical modification detection. The method employs direct RNA sequencing on synthetic RNA sequences, various outputs. Basecalled RNA reads are aligned to reference synthetic RNA sequences to obtain sequence alignment reads. Nucleotide assignments of the sequence alignment reads are then refined, data segmented and the segmented data aligned to the individual k-mers. Raw signal features corresponding to specific nucleotide positions in the reference synthetic RNA sequence are then identifiable. The features of the raw signals are subjected to a multiple-instance supervised learning model training framework for the detection of one RNA chemical modification or multiple RNA chemical modifications. The trained model infers from an unseen RNA sequence data set the likelihood of one RNA chemical modification or multiple RNA chemical modifications.

This invention discloses a method for evaluating the egg production performance of Leizhou Black Ducks. By directly sequencing the FRRS1L gene and detecting single nucleotide polymorphisms, this invention identified multiple molecular markers and haplotypes associated with the egg production performance of Leizhou Black Ducks (starting weight, starting egg weight, and 300-day egg production). These findings can provide a scientific basis for the conservation, breeding, and development of Leizhou Black Ducks, and lay the foundation for the subsequent construction of a high-yielding core population.

The present invention discloses a method to quantify tRNA abundance and tRNA modifications in an RNA sample that comprises contacting RNA with oligonucleotides in the presence of a ligating agent and performing nanopore direct sequencing. It also discloses a kit to perform said method.

Disclosed are nucleic acid analysis and sequencing technologies. More particularly, it concerns compositions and methods for capture, enrichment, adaptation, and direct sequencing of short RNA molecules, including microRNAs (miRNAs), using sequencing platforms. Disclosed are methods of preparing a sequencing library for a target short RNA and kits. The methods further comprising sequencing a cassette comprising the target short RNA using a sequencing platform.

The application discloses a base recognition method and system based on a full convolution network, a medium and a program, and belongs to the technical field of base recognition. The method comprises the following steps: constructing a base calling model based on a DenseNet convolutional neural network; constructing a data set to train the base calling model; collecting an electrical signal of a base to be recognized; inputting the electrical signal into the trained base calling model for recognition to obtain a sequence of the base to be recognized. The base calling model provided by the application significantly improves the base calling accuracy of direct RNA sequencing through an innovative full convolution network architecture and species-specific model training, overcomes many defects of the prior art, and has a wide application prospect and remarkable beneficial effects.

This invention discloses an InDel molecular marker associated with growth traits in Haimen goats and its applications, belonging to the fields of biotechnology and livestock breeding. The InDel molecular marker is a 58bp ins mutation located at position 67616252bp in the genomic sequence of the PPP1R13B gene. This invention uses Haimen goat blood genomic DNA as a template and a direct sequencing method of PCR products to determine genotype. Haimen goats with the ID genotype exhibit excellent growth traits and can serve as an effective molecular marker for improving growth traits in Haimen goats. The detection method of this invention is simple, rapid, accurate, and inexpensive, which can improve the breeding efficiency of Haimen goats and has high application value.

The invention belongs to the technical field of Hu sheep molecular marker-assisted breeding, and particularly relates to application of a CNGA3 gene molecular marker g.39045A > C in Hu sheep molecular marker-assisted breeding. According to the invention, Hu sheep is taken as a research object, PCR amplification, direct sequencing of products and sequence analysis are adopted, CNGA3 gene polymorphism is analyzed, and correlation between different genotypes of polymorphic sites and different growth traits is comprehensively analyzed. An analysis result shows that g.39045A > C is remarkably related to the body length of the Hu sheep, and the body length of the AA genotype and the body length of the CC genotype are remarkably higher than the body length of the AC genotype (P > 0.05).

The present invention provides materials and methods for RNA sequencing and analysis of both polyadenylated and non-polyadenylated RNA molecules.

This invention belongs to the fields of molecular biology and molecular marker technology, and relates to a SNP molecular marker for the FHL3 gene promoter associated with meat production traits in pigs and its application. The genetic marker is cloned from locus 93990293 on pig chromosome 6. Whole-genome DNA was extracted from pig blood, and primers were designed based on the pig genome sequence (NC_010448.4) published in the NCBI database. A C or T base substitution exists at position 585 of the primer amplification sequence, leading to polymorphism at this position. Genotyping of the SNP locus using direct sequencing technology and association analysis showed that, compared to individuals with other genes, individuals with the CC genotype at position 585 had higher birth weight, larger eye muscle area, shorter time to reach 100 kg, and less backfat thickness. This invention provides a new marker for marker-assisted selection in pigs, and its application can accelerate the process of improving high-quality pig breeding.

This invention discloses a human SLC25A13 gene detection kit and its application, including primer and probe sets for eight related sites: c.851_854deL4, c.1638_1660dup, IVS6+5G>A, IVS16ins3kb, IVS4ins6kb, IVS11+1G>A, c.1399C>T, and c.1078C>T. The probe design for the c.1638_1660dup site employs a competitive anti-slip design, enabling the nucleic acid combination 2 at this site to effectively distinguish between heterozygous and homozygous mutations at the c.1638_1660dup site. The kit provides reliable genotyping results with 100% consistency with direct sequencing, exhibiting higher sensitivity than traditional sequencing methods. Furthermore, it is simple and rapid to operate, facilitating large-scale deployment.

The invention belongs to the field of mitochondrial genetic defect disease diagnosis, and particularly relates to a mitochondrial genome methylation level detection method. According to the invention, a mitochondrial separation and purification technology suitable for single-molecule DNA sequencing is innovatively researched and developed, a mitochondrial genome DNA ring is innovatively opened for single-molecule direct sequencing, and mitochondrial genome DNA methylation analysis is further developed. Statistic difference analysis is respectively carried out on a methylation result of a CpG site of a sample mitochondrial genome DNA (mtDNA) obtained by adopting the detection method and a methylation result obtained by adopting a bisulfate Sequencing technology, and the methylation results obtained by the two methods have no significant difference. Compared with bisulfate Sequencing, the method disclosed by the invention has the obvious value advantages of low cost, high flux and short period.

The present application belongs to the technical field of livestock breeding, and particularly relates to a detection method of an insertion / deletion marker of an IRF3 gene of a Shaanbei white cashmere goat and application thereof. The present application takes whole genome DNA of the Shaanbei white cashmere goat as a template, designs a primer combination based on a specific sequence of a regulation region of the IRF3 gene, and realizes efficient, accurate and economical detection of an insertion / deletion polymorphism of a target gene by using molecular biology technologies such as polymerase chain reaction amplification, agarose electrophoresis separation and direct sequencing analysis. The present application is the first to find that the IRF3 gene is significantly related to brucellosis resistance of the Shaanbei white cashmere goat, and can be used as an effective DNA marker for genetic breeding of the Shaanbei white cashmere goat against brucellosis.