To assess the co-accessibility effect of cell-type-specific
trans-open chromatin regions on Z-scores we used the output of Signac’s
CallPeaks() function to retrieve from which cell-type a peak was called by MACS2
21 (link) (implemented in Signac). The cell-types were categorised in 4 broader classes representative of the UMAP and dendrogram:
Lymphoid; CD8 Naive, CD4 Naive, CD4 TCM, CD8 TEM, CD8 TCM, CD4 TEM, MAIT, Treg
NK cells; gdT, NK, CD8 TEM, MAIT
Monocytes; CD14 Mono, CD16 Mono, cDC2, pDC
B cells; B intermediate, B memory, B naive
For ATACseq peaks that were called in all 4 broad cell-type classes, no filtering was done. For ATACseq peaks with some specificity (i.e., not called in all 4 broad cell-type), we removed all
trans-peaks from the
trans-peak pool to match the
cis-peak that were also called in the same broad cell-type class. Therefore, a tested ATACseq peaks called only in B cells and Monocytes by MACS2 would have a null distribution composed of
trans-peaks called in lymphoid and/or NK cells.
