GSE171312
Nanopore Direct RNA sequencing of mice hippocampal brain tissues
Oxford Nanopore enables direct RNA sequencing allowing for base calling of RNA modifications. However, current direct RNA sequencing protocols may not be detecting some classes of non-coding RNAs such as SINE RNAs produced by Short Interspersed Nuclear Elements (SINEs). Using mouse hippocampi RNA samples, we have established a novel Nanopore direct RNA-seq protocol that in addition to long poly A selected RNAs allows sequencing also of non-poly A RNAs as well as short RNAs < 200nt (including SINE RNAs and other non poly A non coding RNAs). We provide here as a resource the first direct RNA-sequencing performed in mouse brain tissues that includes both mRNAs and non poly A or short non-coding RNAs such as SINEs. Overall design: In this study, we employed a transgenic mouse model of amyloid pathology, APP NL-G-F (APP) (Saito et al., 2014) and the respective wild type control C57BL/6J (WT). We have tested mice at the stage of symptom manifestation (that coincides with the active neurodegeneration phase and appearance of amyloid plaques (6 months - 6m/ APP: 3x mice, WT:3x mice), The mice were then sequenced by Nanopore sequencing direct RNA SQK-RNA_002 protocol using the PromethION platform.