Chromatin profiling of HUVECs

We analyzed SOX9 binding and the global effect of SOX9 overexpression on chromatin accessibility and enrichment of histone modifications (H3K4me1, H3K27ac, H3K27me3, H3S28P) by CUT&RUN, CUT&Tag, and ATAC-seq of HUVECs transduced with SOX9 expression plasmid or an empty vector control. Cells were transduced with plasmids and 4 days after they were harvested for CUT&RUN, CUT&Tag, or ATAC-seq. For the time-course SOX9 CUT&RUN and ATA-seq, cells were harvested at the indicated times after transduction. 500 000 cells were used per CUT&RUN and CUT&Tag experiment and 100 000 cells were used per ATAC-seq experiment. Sample quality control was performed using the Agilent 2100 Bioanalyzer. CUT&RUN samples were prepped following the standard protocol for the NEBnext DNA Ultra ii (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 with Paired End 42bp × 42bp reads and Illumina NextSeq 2000 with Paired End 61bp x 61bp.