title: ATAC-seq of human ALK negative ALCL cell line (TLBR2) in parental and HELLS knockdown conditions
design: ATAC-seq of human ALK negative ALCL cell line (TLBR2) in parental and HELLS knockdown conditions
library_construction_protocol: 50'000 cells were collected for ATAC-seq. Cell pellet was lysed in ATAC-seq Lysis Buffer then diluted in ATAC-seq Wash Buffer.  Tagmentation was performed with Illumina Tagment DNA (TD) TDE1 Enzyme and Buffer (Illumina). Nuclear pellet was resuspended in Transposition Mix and incubated at 37Â°C. Cells were cultured in RPMI medium supplemented with 10% FBS, 1% P/S and 20U IL-2. Functional HELLS knockdown by shRNA was induced by the treatment with Doxycycline (DOX) for 48h at final concentration of 100ng/ml. DNA was purified using DNA Clean and Concentrator-5 KIT (Zymo Research). Fragmented DNA amplification and barcoding was performed with NEBNext Ultra II Q5 2X Master Mix (New England Biolabs) with sample-specific adapters. Samples were quantified with NEBNext Library Quantification kit (New England Biolabs) and amplified for an additional 7 cycles.