title: RNA-seq with metabolic labelling of human lymphoblast cell line K562 treated with a panel of 83 different epigenetically active compounds and untreated controls
design: RNA-seq with metabolic labelling of human lymphoblast cell line K562 treated with a panel of 83 different epigenetically active compounds and untreated controls
library_construction_protocol: The experiments used K562 cells from DSMZ (ACC-10) K562 cells were were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% antibiotics consisting of a Penicillin/ Streptomycin combination at 37Â°C and 5% CO2. Cells were grown in T25-flasks, seeded to a density of 200,000 cells/ ml and split 1:4 once the density approached 1,000,000 cells/ ml. Cells were treated with compounds from a panel of epigenetically active drugs at a concentration of 12.5 micromolar either one or three hours before harvesting. Additionally, 200 micromolar 4sU was added one hour before cell harvest. RNA was isolated using magnetic beads following the BOMB-bio protocol 8.2 version 1.0 The sequencing libraries were prepared from isolated RNA through mRNA capture with an oligo-dT primer, and full length cDNA molecules were constructed through the use of a template switching oligo. The resulting cDNA fragments were pre-amplified through PCR and then fragmented through tagmentation to yield sequence ready fragments.