nkx2.1.incluster13_distalPeaks_PAL.bed.highestScoreMotifs

NKX2-1 transcription factor binding site (TFBS) analysis. First, we used HOMER to identify predicted NKX2-1 binding sites (using the HOMER built in matrix “nkx2.1.motif”) across the GRCh38 genome, and removed any site within the ENCODE blacklist. For normal lung cell analysis, we intersected this list with 6,754 ATAC-seq peaks identified in the pneumocyte (PAL) cluster 13 CREs from (6) (downloaded from supplemental table 6 of that paper “Table_S6_Union_set_of_cCREs.xlsx”). We then selected 5,974 peaks that overlapped a predicted NKX2-1 TFBS, and centered each on the predicted NXK2-1 TFBS. If multiple TFBS were present in the peak, we took the motif with the highest HOMER log-odds match score.