GSM8208877: ATAC WT, donor1; Mustela putorius furo; ATAC-seq
Fully differentiated WT and CF ferret PDE cultures grown at ALI for 14 days were dissociated using Accutase. Cells were dissociated using Accutase and ~50,000 cells from each PDE culture were lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40: Sigma). Transposition was performed using 25 μl tagmentation reaction mix from Tagment DNA kit (Illumina, CA, USA). Tagged DNA was amplified indexed, using the NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs, MA, USA) and with Nextera DNA CD Indexes (Illumina, CA, USA), using the following settings: 72°C for 5 minutes; 98°C for 30 seconds; 12 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. The indexed library was purified with 1.8 times the volume of Ampure XP beads (Beckman Coulter, CA, USA). Library quality was assessed using a BioAnalyzer 2100 High Sensitivity DNA Chip (Agilent Technologies, MA, USA). All DNA libraries that exhibited the correct nucleosome pattern were pooled and processed for 150bp paired-end sequencing using a HiSeq4000 (Illumina) in the University of Iowa Genomics Division. Cells were dissociated using Accutase and ~50,000 cells from each PDE culture were lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40: Sigma). Transposition was performed using 25 μl tagmentation reaction mix from Tagment DNA kit (Illumina, CA, USA). Tagged DNA was amplified indexed, using the NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs, MA, USA) and with Nextera DNA CD Indexes (Illumina, CA, USA), using the following settings: 72°C for 5 minutes; 98°C for 30 seconds; 12 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. The indexed library was purified with 1.8 times the volume of Ampure XP beads (Beckman Coulter, CA, USA).