Illumina HiSeq 4000 paired end sequencing; Studying changes in chromatin accessibility in A549 cells by ATAC-seq directly after 20-hour glucocorticoid treatment and following a 24-hour hormone washout
Studying changes in chromatin accessibility in A549 cells by ATAC-seq directly after 20-hour glucocorticoid treatment and following a 24-hour hormone washout
ATAC-seq was performed with 100,000 cells per treatment, cells were grown in DMEM containing 5% fetal bovine serum. A549 cells where grown to approximately 90% confluence according to standard protocols in DMEM medium with 5% FBS. Cells were treated for 20 hours with 100 nM demxathasone, 100 nM hydrocortisone or 0.1% ethanol and either harvested immediately or washed 2x with PBS and subsequently cultured in hormone-free medium for 24 hours before harvest. ATAC-seq was performed with 100,000 cells per treatment according to the Omni-ATAC-seq protocol [PMID: 28846090]. DNA was extracted using the DNA Clean & Concentrator Kit (Zymo research #D4014). Library amplification involved 11 PCR cycles using the NEBNext High-Fidelity 2x PCR Master Mix (New England Labs, Cat #M0541).