GSM5174367: pre-adipocyte WT; Mus musculus; ATAC-seq
Apologies for the delay in replying my amendments as requested are below: Differentiating cells were lysed directly in the cell culture plate. Lysis buffer was added directly onto cells grown in a 12-well plate. Plates were incubated on ice for 10min until cells were permeabilized and nuclei released. Lysis buffer was gently pipetted up and down to wash nuclei off the well and transferred into a chilled 1.5ml tube to create crude nuclei. Nuclei were spun down at 600 x g for 10 min at 4°C, nuclei pellets were then re-suspended in 40ul TD Buffer, nuclei counted using trypan blue and volume of 50.000 nuclei was determined. Transposition reaction was performed following a previously published protocol (72). Tagmented DNA was PCR amplified for 11. Quality was assessed using a DNA1000 Chip (Applied Biosystems) and run on a Bioanalyzer (Applied Biosystems). The profiles showed that all libraries had a mean fragment size of ~190bp and characteristic nucleosome patterning, indicating good quality of the libraries.