GSM8558850: ATAC-seq WT r1; Mus musculus; ATAC-seq
The ATAC-seq reaction was performed with 50,000 cells as previously described (Buenrostro et al., 2013) with minor adjustments of the protocol, using the Nextera DNA Library Prep Kit (Illumina) together with the barcoded primers from the Nextera Index Kit (Illumina). An additional size selection step was performed after the first 5 cycles of library amplification. For this, the PCR reaction was incubated with 0.6 x volume of Ampure XP beads (Beckman Coulter) for 5 min to allow binding of high molecular weight fragments. Beads containing long DNA fragments were separated on a magnet and the supernatant containing only small DNA fragments below roughly 800 bp were cleaned up using MinElute PCR purification columns (Qiagen). All libraries were amplified for 12 cycles in total, visualised and quantified with a TapeStation2200 (Agilent)