GSM4907309: 0.2 kPa - rep2; Mus musculus; ATAC-seq
FACS sorted mouse GFP+ lung fibroblasts were seeded (5,000 cells/cm2) onto 0.2 kPa PDMS, 32 kPa PDMS (Advanced Biomatrix, San Diego, CA, USA), or tissue-culture plastic. All culture plates were identically coated with collagen I (0.1 mg/mL diluted in PBS) (Advanced Biomatrix, San Diego, CA, USA) for one hour at room temperature. Cells were cultured for 8 days. Fibroblasts were then trypsinized and counted. 50,000 cells were subjected to Omni ATAC-seq following the published protocol22. The size of library DNA was determined from the amplified and purified library by a Fragment Analyzer (Advanced Analytical Technologies; AATI; Ankeny, IA), and the enrichment of accessible regions was determined by the fold difference between positive and negative genomic loci using real-time PCR. The following primer sequences were used: accessibility-positive control locus: AT-P7-F: 5'- GGCTTATCCGGAGCGGAAAT -3′, AT-P7-R: 5'-GGCTGGAACAGGTTGTGTTG -3′. Accessibility-negative control locus: AT-P13-F: 5'-TCCCCTTTACTGTTTTCCTCTAC-3′, AT-P13-R: 5'-GGATTGATGAGGAAACAGCCTC-3′. The libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 instrument (Illumina, San Diego, CA, USA).