Project description:Alternative splicing diversifies mRNA transcripts in human cells. While the spliceosome pairs exons with a high degree of accuracy, the rates of rare aberrant and non-canonical pre-mRNA splicing have not been evaluated at the nucleotide level to determine the quantity and identity of these events across splice junctions. Using ultra-deep sequencing the frequency of aberrant and non-canonical splicing events for three splice junctions flanking exon 7 of SMN1 were determined at single nucleotide resolution. After correction for background noise introduced by PCR amplification and sequencing steps, pre-mRNA splicing was shown to maintain a low overall rate of aberrant and non-canonically spliced events. Several previously unannotated splicing events across 3 exon|intron junctions in SMN1 were identified. Mutations within SMN exon 7 were shown to affect splicing fidelity by modulating RNA secondary structures, by altering the binding site of regulatory proteins and by changing the 5’ splice site strength. Mutations also create a truncated SMN1 exon 7 through the introduction of a de novo non-canonical 5’ splice site. The results from the ultra-deep sequencing approach highlight the impressive fidelity of pre-mRNA splicing and demonstrate that the immediate sequence context around splice sites is the main driving force behind non-canonical splice site pairing.

2019-09-24 | GSE137883 | GEO

Deciphering KRAS and NRAS mutated clones dynamics in MLL-AF4 pediatric leukemia by ultra deep sequencing analysis

Project description:We studied the KRAS and NRAS mutational status in pediatric MLL-AF4+ leukemia patients by means of ultra deep amplicon sequencing. The gene expression profiles of RAS wild type and RAS mutated patients were investigated by gene expression analysis. We showed that mutated patients were characterized by a RAS related expression signature.

2016-10-04 | GSE77416 | GEO

A Nile Rat Transcriptomic Landscape Across 22 Organs By Ultra-deep Sequencing and Comparative RNA-seq pipeline (CRSP)

Project description:We generated the first ultra-deep Nile grass rat RNA-seq data from 60 biopsy samples representing 22 major organs, providing a unique resource and spatial transcriptomic reference (e.g., tissue gene expression baseline) for using Nile grass rat as a model to study human diseases.

2022-12-09 | GSE215233 | GEO

Ultra high resolution array painting

Project description:Ultra high resolution breakpoint mapping using custom oligonucleotide arrays and array painting Keywords: Breakpoint mapping

2006-11-01 | GSE4297 | GEO