Want to perform ATAC-seq in the lab for genome wide mapping of open/accessible chromatin to find out which genes are likely expressed? This could be a good complement to RNA-seq of the same sample where you could potentially link upstream open chromatin confirmation to downstream gene expression. Here is some more information on the technique: https://www.activemotif.com/blog-atac-seq
I used this wet-lab protocol to attain high quality ATAC-seq data from FACS-purified human microglia in a humanised mouse model of Alzheimer's disease. I used 50,000 cells per sample (100,000 cells per sample would also work for this protocol). I had a mean FRiP score (fraction of reads in peaks) of 0.7 from 20 samples (usually FRiP >0.3 is good). This protocol does not include the analysis pipeline - perhaps our friends over at bioinformatics can help;) Happy to answer any questions and have fun seq-ing!