title: GSM9589238: Ranbp2 Wildtype ATAC-seq Replicate 2; Mus musculus; ATAC-seq
library_construction_protocol: The ATAC-seq was performed as per the previously published Omni-ATAC protocol. Briefly, 50,000 10T ½ cells were pelleted at 500 g for 5 minutes and subsequently resuspended in 100 µl ATAC-resuspension buffer containing 0.5% NP40, 0.5 % Tween-20 and 0.01% Digitonin. The cells were incubated on ice for 10 minutes and then 1 ml of cold ATAC-RSB containing 0.1% Tween 20 was used to wash the cells. The nuclei were pelleted at 500 g for 5 minutes, the supernatant was carefully removed, and the nuclei were resuspended in 50 µl transposition mixture containing 25 µl of 2x TD buffer, 16.5 µl of PBS, 5 µl nuclease free water, 0.5 µl of 1% digitonin, 0.5 µl of 10% Tween-20 and 2.5 µl of transposase (Illumina Tagment DNA enzyme 1, Catalogue number 20034198). Transposition was performed by incubating the mixture at 37°C for 30 minutes in a thermoshaker, after 30 minutes, the DNA was extracted using the NEB Monarch® PCR & DNA cleanup kit (Catalogue number T1030L). Libraries were generated by performing PCR using the Illumina/Nextera primers after which Ampure XP beads were used for library cleanup, and the DNA libraries were subsequently sequenced on the Illumina NextSeq platform with 75bp Paired-End sequencing.
identifiers.namespace: GEO
identifiers.id: GSM9589238_r1