Transcriptome sequencing of rTg4510 AD mouse model

This directory is a repository of scripts pertaining to whole transcriptome profiling and targeted sequencing of rTg4510 mice, and form the source of the paper: Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology by SK.Leung, A.R.Jeffries,..E.Hannon,J.Mill.

Summary

• Following global Iso-Seq transcriptome profiling performed on rTg4510 wild-type (WT) and transgenic (TG) mice using Sequel (PacBio), data from each sample (1 per flow-cell) was merged and processed using Iso-Seq3 pipeline, aligned to reference genome (mm10) and annotated using SQANTI3.
• Following targeted sequencing of rTg4510 WT and TG mice across 20 dementia- and AD-asociated genes using Sequel (PacBio) and MinION (ONT), respective data was processed using technology-specific pipelines, and merged.
• Merged transcriptome of 20 AD-genes further characterised using FICLE and long-read proteogenomics pipeline
• Differential expression analysis was performed at a global and targeted level to identify transcript expression changes associated with development of tau pathology in these mice
• Fluorescence-activated nuclei sorting (FANS) followed by ONT nanopore sequencing was used to profile full-length transcripts in purified NeuN+ (neuron-enriched) and NeuN- (glia-enriched) cortical nuclei populations isolated from a subset of mice (n = 8, 2 WT and 2 TG at ages 2 and 8 months).

Datasets

1. Whole Iso-Seq Transcriptome (n = 12 samples)
2. Targeted Iso-Seq Transcriptome (n = 24 samples)
3. Targeted ONT Transcriptome (n = 18 samples)
4. Whole RNA-Seq Transcriptome (n = 59 samples)
5. Targeted ONT Transcriptome from FANS dataset (n = 8 samples)

The processed intermediate datafiles and UCSC genome browser tracks (merged mouse targeted data, mouse whole transcriptome Iso-Seq data, mouse sorted data and human AD targeted data) are available for download at Zenodo.

Publications

• Leung et al. (2023): Targeted transcriptome sequencing (ONT and PacBio) of rTg4510 mice across 20 dementia-associated genes
• Leung, Jeffries et al. (2021): PacBio Whole Iso-Seq transcriptome sequencing of rTg4510 mice
• Castanho et al. (2020): RNA-Sequencing of rTg4510 mice