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 the HDAC inhibitor SAHA (vorinostat) at a dose of 10 micromolar for either 6 or 24 hours. No 4sU was used in this experiment. 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.