Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Optimization of ONT Sequencing on meta-genomics samples

ABSTRACT: The effect of amplicon length on Taxonomic Analysis of Oxford Nanopore Sequencing

PROVIDER: PRJEB33392 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Identification of reproduction-related genes in the hypothalamus of the sheep (Ovis aries) using the ONT full-length transcriptome sequencing technology

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).

2024-11-20 | GSE275445 | GEO

Detailed analysis of the murine-aged brain transcriptome [ONT]

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.

2024-03-13 | GSE233836 | GEO

Direct long-read RNA sequencing of Raji cells

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.

2023-12-08 | GSE243920 | GEO

Direct RNA ONT sequencing of pine roots under ammonium nutrition

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.

2021-05-22 | GSE174830 | GEO

Nanopore sequencing of K562 for DNA cytosine modification detection

Project description:Nanopore sequencing of K562 human cell line using the Oxford Nanopore GridION and R9.4.1 version chemistry

2021-09-20 | GSE173688 | GEO

Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19

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.

2020-05-19 | GSE136068 | GEO

Comparing Nanopore MinION and Ion torrent sequencing of the 16S rRNA gene for marine samples using different pipelines and databases

Project description:16S marine amplicon - Oxford Nanopore versus Ion Torrent

| PRJEB48749 | ENA

LoRTIS: A long read method for analysis of large transposon mutant libraries

Project description:Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described to date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where the repeat units are longer than the sequence read length. To overcome this limitation, we have developed a TIS method using Oxford Nanopore sequencing technology that generates and uses long nucleotide sequence reads; we have called this method LoRTIS (Long Read Transposon Insertion-site Sequencing). This experiment data contains sequence files generated using Nanopore and Illumina platforms. Biotin1308.fastq.gz and Biotin2508.fastq.gz are fastq files generated from nanopore technology. Rep1-Tn.fastq.gz and Rep1-Tn.fastq.gz are fastq files generated using Illumina platform. In this study, we have compared the efficiency of two methods in identification of transposon insertion sites.

2022-05-30 | E-MTAB-11351 | biostudies-arrayexpress

Project description:Oxford Nanopore full-length HIV sequencing reads

| PRJNA765218 | ENA

Oxford nanopore sequencing data from the Arabidopsis thaliana accessions Ler-0, Cvi-0 and Tanz-1

Project description:Oxford nanopore sequencing data from the Arabidopsis thaliana accessions Ler-0, Cvi-0 and Tanz-1

2022-08-06 | E-MTAB-12009 | biostudies-arrayexpress