title: Illumina NovaSeq 6000 paired end sequencing; ATAC-seq of MUTZ3 cells in experiments to investigate EVI1 regulation
design: ATAC-seq of MUTZ3 cells in experiments to investigate EVI1 regulation
library_construction_protocol: 100.000 cells (MUTZ3, MOLM1) were lysed in lysis buffer  The MUTZ3 cell lines were cultured in αMEM (HyClone) with 20% fetal calf serum (FCS) and 20% conditioned 5637 medium. The 293T were cultured in DMEM (Gibco) with 10% FCS. All cell lines were supplemented with 50 U/mL penicillin and 50 μg/mL streptomycin. Viable frozen AML cells were thawed and resuspended in IMDM medium supplemented with: 20% BIT medium (Stem cell technologies), 1x β-mercaptoethanol (1000x Life technologies), 6 µg/ml LDL (Sigma Aldrich), human IL6, IL3, G-CSF, GM-CSF at 20 ng/ml and FLT3, SCF at 50 ng/ml (Peprotech). Immediately after lysis, nuclei were spun at 500g for 8 minutes at 4°C. After pelleting the nuclei, we the nuclei were resuspended in Tn5 transposase reaction mix (25 ul 2X TD buffer, 2.5 ul Tn5 transposase, and 22.5 ul nucleasefree water). The transposition reaction was performed at 37°C for 30 minutes. Immediately after the transposition reaction, DNA was purified using a Qiagen MinElute kit.  The transposed library was PCR amplified using Nextera primers. The PCR reaction was subsequently cleaned up using AMPureXP beads.