ATAC sequencing of (1) isolated lung endothelial cells (iLECs) from wildtype and Zmiz1-KO endothelial cells and (2) control and Zmiz1 siRNA treated TeloHAECs cells

ATAC sequencing library was prepared as per manufacturer instruction (Active Motif, 53150). Briefly, intact nuclei were isolated. Samples were treated with a hyperactive Tn5 transposase which tag the target DNA with sequencing adapters and fragment the DNA simultaneously.

Library was then quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32851) and verified using the Bioanalyzer DNA High Sensitivity Assay Kit (Agilent, 5067-4626). Validated samples were sequenced using the NextSeq1000/2000 P2 Reagents (100 Cycles) v3 (Illumina, 20046811) on a Nextseq1000/2000. Resulting sequencing data were analyzed using basepairtech ATAC-Seq pipeline (www.basepairtech.com).

Briefly, sequenced reads were aligned to the human (hg19) or mouse (mm10) reference genome using Bowtie2. ATAC-Seq peaks and differentially accessible regions were quantified using MACS2 and DESeq2. Results: ATAC seq peaks analysis using MACS2 identified thousands of peaks of which are mostly located in intergenic, introns, and promotors regions.

Conclusions: We assessed Zmiz1 mediated regulation of chromatin accessibility isolated lung endothelial cells and TeloHAECs.