Datasets

[tavareshugo]

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

[tavareshugo]

Could use a separate dataset for demonstrating CUT&RUN.

• Drosophila (small genome): https://www.tandfonline.com/doi/full/10.1080/19336934.2023.2209481#d1e348
• GEO accession: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211269

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.