GSM6654455: SMF110_SEM_dCas9-KRAB-BSD_sgFLT3_DE-1_Rep2_ATACseq; Homo sapiens; ATAC-seq
Briefly, 10,000 of SEM cells were treated with transposition mix consisting of 22 μL nuclease-free water; 25 μL 2 × TD Buffer; 2.5 μL TDE1 transposase; and 0.5 μL of 1% digitonin (added immediately before removing the supernatant from cell pellets), followed by incubation at 37°C on an Eppendorf ThmorMixer at 300 rpm for 30 minutes. DNA was purified with using the MinElute Reaction Cleanup Kit (Qiagen, 28204) and amplified for 5 cycles using the PCR mix composed of 10 μL transposed DNA, 2.2 μL nuclease-free water, 6.25 μL 10 μM barcoded Nextera primer-F, 6.25 μL 10 μM barcoded Nextera primer-R, 0.3 μL 100 × SYBR Green I (Invitrogen, S-7563), and 25 μL NEBNext® High-Fidelity 2 × PCR Master Mix (NEB, M0541). PCR products were subsequently re-amplified for another 6 PCR cycles, followed by purification using SPRIselect beads (Beckman Coulter, B23317). Paired-end sequencing (2 × 100 bp) was performed using the Illumina HISeq 4000 platform. Paired-end reads were analyzed using cutadapt (version 1.18) for adaptor trimming and then mapped to the human hg19 genome by Bowtie2 (version 2.2.9)