title: Illumina HiSeq 2000 sequencing; ATAC-seq for L3.6pl cells
design: ATAC-seq for L3.6pl cells
library_construction_protocol: ATAC was performed following the protocol of Buenrostro et al. Briefly, 50,000 L3.6pl cells were trypsinized and washed twice with cold PBS. Then cells were re-suspended in lysis buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and incubated for 15 minutes at a rotating wheel at 4ºC followed by centrifugation and in re-suspended in 50 µl of transposition mix composed of 2.5µl of TDE1 (Nextera Tn5 Transposase), 25 µl TD (2x reaction buffer) in nuclease free water (Nextera DNA Library Prep Kit, FC-121-1030, Illumina). Then it was incubated at 37 degrees for 30 minutes. MinElute PCR Purification kit (Qiagen) was used for DNA extraction following the instructions of the manufacturer.  ATAC libraries were made using the Nextera DNA Library Prep Kit according to Buenrostro et al. The libraries were amplified for 15 cycles in total of: 98ºC for 10 seconds, 63ºC for 30 seconds, and 72ºC for 60 seconds.
attributes.tag: Experimental Factor: replicate
attributes.value: 1