Fresh crypts were extracted and dissociated into single cells. 50,000 cells were sorted and pelleted by centrifugation for 5 min at 500 g and 4°C. Cell pellets were washed once with 1xPBS and pelleted again. Cell pellets were resuspended in 25 µl of lysis buffer and nuclei were pelleted. Supernatant was discarded and nuclei were re-suspended in 50 µl reaction buffer containing 2.5 µl of Tn5 transposase and 25 µl of TD buffer. Sequencing libraries were prepared using DNA purification (QIAquick minelute columns, Qiagen) and amplification by PCR using Nextera complimentary primers. Paired-end sequencing was performed on an Illumina HiSeq 2000 machine by multiplexing three samples on one lane.