Project description:the hypothalamus tissues of high-reproduction small-tailed Han sheep and low-reproduction Wadi sheep were collected, and full-length transcriptome sequencing by Oxford Nanopore Technologies (ONT) was performed to explore the key functional genes associated with sheep fecundity. The differentially expressed genes (DEGs) were screened and enriched using DESeq2 software through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).
Project description:In this work, we collected and analyzed two cohorts of young-adult and aged-adult mice brain mRNAs and determined their levels using second- (illumina) and third-generation (Oxford Nanopore) sequencing technologies. We report a transcriptome-wide study of differential transcript usage during brain aging. In addition, we provide the community with a large resource of whole brain transcriptomes and comprehensive analyses that identify widespread diversity of mRNAs during aging.
Project description:Genome-wide 5-methylcytosine (5mC) profiling at CpG dinucleotides in Hydra viridissima using Oxford Nanopore long-read sequencing with Dorado base modification detection. Five ONT runs (one symbiotic, four aposymbiotic clone 2) were basecalled with Dorado sup,5mCG_5hmCG, aligned to Carnegie v1 genome assembly (JBWVZK000000000), and methylation quantified with modkit. Global CpG methylation is ~9-10%, bimodal (88% unmethylated, 7% fully methylated). Unique genomic regions show higher methylation (12%) than repetitive regions (7.5%).
Project description:Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection
Project description:To identify full-length cap-to-poly(A) mRNA isoforms of CD20 and rule out reverse transcription artifacts which are common in cDNA-seq approaches, long-read Oxford Nanopore direct RNA sequencing was performed on the Raji cell line.
Project description:Epitranscriptomics modifications constitute a gene expression checkpoint in all living organism including plants. Considering the relevance of nitrogen nutrition and metabolism for the correct plant growth and development, it can be hypothesized that epitranscriptome changes must regulate every biological process in plants including nitrogen nutrition. In the present work, the epritranscriptomics changes in maritime pine roots caused by ammonium nutrition have been monitored through direct RNA sequencing using Oxford Nanopore Technology. The main transcriptome responses to ammonium nutrition affected to transcripts involved in nitrogen and carbon metabolisms, defense response, hormone synthesis and signaling, and translation. Additionally to a global detection of epitranscriptomics marks, the m6A deposition and its dynamics have been identified, which seems to be important regulators of translation when compared with the proteomic profiles of the same samples. In this sense, the obtained results suggest that protein translation is finely regulated through the epitranscriptomics marks maybe through changes in mRNA polyA length, transcript amount and ribosome protein composition. The multiomics results in the present study suggest that the epitranscriptome must modulate the responses to development and environmental changes, including ammonium nutrition, through buffering, filtering and focusing the final products of the gene expression.
Project description:We report that retention of intron 2 which affects expression of CD19 in CART-19 relapsed leukemia occurs in the context of full length CD19 transcript using Oxford Nanopore sequencing technology. By performing Direct RNA sequencing on Reh leukemia cell lines, we showed that intron 2 retention is functionally equivalent to nonsense mutations.