title: GSM3902503: ATAC-seq_Experiment 1 - control condition (24h); Homo sapiens; ATAC-seq
library_construction_protocol: ATAC-seq assay was performed in 4 independent replicates for each time point (2 and 24 hours) as previously described in (Buenrostro, et  al. 2013). Briefly, 50,000 cells were isolated from their nuclei by incubating the cells in 300 μl cold lysis buffer for 25 min on ice and resuspending them after 5 and 15 min using a syringe with a 29G needle. The pellet was next washed in 100 μl of lysis buffer and centrifuged for 15 min at 500 g at 4°C. The transposition reaction was carried out in a 25 μl reaction mix containing 2 μl of Tn5 transposase, 12.5 μl of TD buffer (Nextera DNA Library Prep Kit, 15028212, Illumina, San Diego, USA) and 10.5 μl DEPC-treated water. The transposition reaction mix was incubated at 37°C for 1 h following inactivation by incubating for 30 min at 40°C after addition of 5 μl of clean up buffer (900 mM NaCl, 300 mM EDTA), 2 μl of 5% SDS and 2 μl of Proteinase K. Isolation of the tagmented DNA was performed with 2x SPRI beads cleanup (Agencourt AMPure XP, Beckman Coulter) and was eluted in 20 μl DEPC treated water. Two sequential 9-cycle PCR were performed in order to enrich for small tagmented DNA fragments.
attributes.tag: GEO Accession
attributes.value: GSM3902503