title: GSM7426379: DV1; Rattus norvegicus; ATAC-seq
library_construction_protocol: Following treatment, media was aspirated, and cells were washed with 1x cold PBS. Then, 600 µl of Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, Molecular Grade H2O) was added to cell culture wells and incubated for 5 mins on ice. Lysed cells were then transferred to a 1.5 ml Eppendorf tube and centrifuged at 500 g for 10 mins in a swinging bucket centrifuge. Following removal of supernatant containing lysis buffer and cell debris, 500 µl of 1x cold PBS was added to each tube, and nuclei were counted using the Countess II (Life Technologies). The approximate volume needed to achieve 50,000 nuclei was then placed in new Eppendorf tube, and centrifuged at 500 g for 10 mins in a swinging bucket centrifuge. The nuclei pellet was then resuspended in 22.5 µl of tagmentation reaction mix containing Molecular Grade H2O, 2x Tagment DNA Buffer (Illumina), 0.011% Digitonin, 0.1% Tween-20, followed by the addition of 2.5 µl TDE1 (Illumina) and incubated at 37°C for 1 hr. Following tagmentation, libraries were PCR amplified and purified using the Qiagen Minelute PCR purification kit (Qiagen). To remove primer dimers, libraries were bead purified using one round of 1.0X Ampure XP beads with 80% ethanol, followed by a second round of 0.8X Ampure beads with 80% ethanol. Libraries were sequenced (75-bp paired end reads) on the NextSeq500 platform (Illumina).