From a painful pinch to a soft caress, scientists are zooming in on the pressure-sensitive proteins that allow cells to detect tension and pressure.

Integrative Analysis of PBMC scATAC-seq and scRNA-seq

In this example, we will be analyzing two scATAC-seq datasets (5K and 10K) and one scRNA-seq dataset from PBMC. All three datasets are freely available from 10X genomics.


In detail, we will be performing the following analysis:

1. Cell selection for PBMC 5k and 10k scATAC;
2. Randomly sample 10,000 cells as landmarks;
3. Unsupervised clustering of landmarks;
4. Project the remaining (query) cells onto the landmarks;
5. Supervised annotation of scATAC clusters using scRNA dataset;
6. Downstream analysis including peak calling, differential analysis, prediction of gene-enhancer pairing.

10X Adult Mouse Brain

In this example, we will be analyzing a dataset of 5K cells from the adult mouse brain available from 10X genomics.