Open tavareshugo opened 4 months ago
Could use a separate dataset for demonstrating CUT&RUN.
This dataset has both ATAC-seq and CUT&RUN. It could be used as a kind of "capstone" exercise where they use the skills from the course to process these data. Might need some intro to specific software or considerations for CUT&RUN, but many of the concepts will overlap with ChIP-seq, so they can do the exercise by themselves.
This paper looks really nice: https://doi.org/10.1093/nar/gkad1225
Has ChIP-seq, ATAC-seq, RNA-seq, enough replicates, two groups (for differential binding).
SRA: https://www.ncbi.nlm.nih.gov/bioproject/?term=GSE196942