GSM2975802: LPS_4; Mus musculus; ATAC-seq
Samples were prepared for ATAC-Seq essentially as described in Buenrostro et al., 2013. Macrophages were washed twice in cold PBS, scraped in cold PBS, and counted using a hemocytometer. Based on this count, 50,000 cells were aliquoted and pelleted by centrifugation. Cell pellets were washed once with 50 uL cold PBS on ice before lysis in 50 uL hypotonic lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) over the course of a 10 minute spin at 4°C. Pelleted nuclei were resuspended in 50 uL transposition reaction mix with 3 uL Nextera transposase per sample (Illumina). The reaction was stopped with 0.1% SDS and transposase-accessible DNA was isolated using AMPure XP beads (Beckman-Coulter). Accessible DNA was amplified by PCR for 5 cycles, assessed for yield by qPCR as described (Buenrostro et al. 2013) and amplified for an additional 7 cycles.
GEO
GSM2975802