We have generated coIP and ChIP-SICAP datasets for identifying interacting proteins of FLAG-PRDM9 in HEK-P9 system (PRDM9 overexpression system in HEK293 cells). ChIP-SICAP is a novel proteomics method that combines ChIP and stringent washes, to identify chromatin-associated proteins at a high resolution (Rafiee et al., 2016). We have analyzed the proteomics data from ChIP-SICAP and coIP in these ways:
- Plot the SICAP interactors and compare the performance of SICAP to co-IP
- Plot the number of contaminant proteins in SICAP and co-IP
- Overlap the SICAP data with single-cell transcriptomics data obtained from mouse-testes (Jung and Wells et al., 2018).
- Overlap the bulk co-IP and SICAP datasets with single-cell proteomics datasets (Fang et al., 2021) and identify critical regulators of recombination in mouse testes.