Project description:Benchmarking Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for Whole Genome Sequencing for bacterial genomes and use in clinical microbiology
Project description:We performed long-read ONT sequencing and matched RNA sequencing on two Collaborative Cross mouse strains and their F1 crosses. Allele-specific methylation and expression analyses revealed widespread and diverse patterns of intergenerational epigenetic inheritance. Included among these are a large number of non-Mendelian inheritance patterns, many of which have not previously been observed in naturally occurring mammalian genomes. Targeted ONT sequencing of F2 crosses of the same Collaborative Cross strains enabled further characterization and validation of these epigenetic inheritance patterns, including distinguishing those patterns mediated by cis- or trans-acting regulatory factors.
Project description:We performed long-read ONT sequencing and matched RNA sequencing on two Collaborative Cross mouse strains and their F1 crosses. Allele-specific methylation and expression analyses revealed widespread and diverse patterns of intergenerational epigenetic inheritance. Included among these are a large number of non-Mendelian inheritance patterns, many of which have not previously been observed in naturally occurring mammalian genomes. Targeted ONT sequencing of F2 crosses of the same Collaborative Cross strains enabled further characterization and validation of these epigenetic inheritance patterns, including distinguishing those patterns mediated by cis- or trans-acting regulatory factors.
Project description:We developed ONT-cappable-seq, a specialized long-read RNA sequencing technique that allows end-to-end sequencing of primary prokaryotic transcripts using the Nanopore sequencing platform. We applied ONT-cappable-seq to study the transcriptional landscape of Pseudomonas aeruginosa phage LUZ7, leading to a comprehensive genome-wide map of viral transcription start sites, terminators and complex operon structures that fine-regulate gene expression. At the same time, it provides new insights in the RNA biology of LUZ7 and paves the way for more in depth transcription studies that can help unveil the complex layers of phage-host interactions.
Project description:The global transcriptional profiles of Pseudomonas aeruginosa phages LUZ19, LUZ24, YuA, PAK_P3, 14-1 and phiKZ was obtained using the long read RNA sequencing technique ONT-cappable-seq. Using this approach we obtained a comprehensive genome-wide map of viral transcription start sites, terminators and transcription units.