Code associated with Acri et al., 2023 J Exp Med
Code used to analyze data and generate figures for Acri et al., Network analysis identifies strain-dependent response to tau and tau seeding-associated genes (DOI: https://doi.org/10.1084/jem.20230180)
We performed several biochemical and transcriptomic analyses in AAV-TauP301L and AAV-EGFP injected mice from 4 genetic backgrounds (C57BL6/J, CAST/EiJ, PWK/PhJ, WSB/EiJ) all at 6 months of age.
Raw transcriptomic data (fastq and nanostring output) can be found GEO (GSE223840, GSE233988).
The code in this repository is everything which can analyze the data as well as generate all the figures for the paper, both main and supplementary. A full list of figures and where you can find the code for them is below:
| Folder | Script | Figures |
|---|---|---|
| Genetics | BCPW_Circos_AgoraVar.R | 1 |
| Biochem | BCPW qPCR analysis.R | 2C |
| Biochem | BCPW MSD analysis.R | 2D-E |
| Biochem | BCPW Tau FRET analysis.R | 2F |
| Transcriptomics | BCPW RNAseq.R | 3-4 |
| Transcriptomics | BCPW WGCNA_V3_PowerBack6_updatedViz_20221116.R | 5 |
| Transcriptomics | BCPW Gene Signature Comparisons.R | 6 |
| Transcriptomics | BCPW Gene Signature Comparisons v2_for JEM revision.R | 6 |
| Transcriptomics | BCPW Nanostring.R | 7 |