GSM8834934: mammary gland, puberty, stromal; Mus musculus; ATAC-seq
ATAC-seq samples were prepared according to the protocol from Buenrostro et al. Briefly, freshly sorted cells were washed once in 50ul ice-cold PBS and gently resuspended in 50ul cold lysis buffer (10mM Tris-HCl, pH 7.4; 10mM NaCl; 3mM MgCl2 and 0.1% NP-40) to isolate nuclei. The transposase reaction (Illumina Nextera DNA Library Preparation Kit, FC-121-1030) was performed for 30min at 30°C and DNA was purified using MinElute PCR purification columns (Qiagen, #28004). DNA fragments were amplified using NEBNext Ultra II Q5 Master Mix (#M05445) and custom primers (see accompanying publication). The following PCR conditions were used: 72°C for 5min; 98°C for 30sec, 8 cycles of 98°C for 10sec, 63°C for 30sec and 72°C for 1min. Libraries were purified with the MinElute PCR purification kit. An additional, single left-sided purification with AMPure XP beads (Beckman Coulter #A63880) was performed to remove primer dimers. Libraries were quantified with qRT-PCR before paired-end sequencing on an Illumina NextSeq 550 system (2 x 75bp, performed by MAD: Dutch Genomics Service & Support Provider, Swammerdam Institute for Life Sciences, University of Amsterdam).
GEO
GSM8834934_r1