Gene expression

Total RNA was isolated using RNeasy-Plus Mini kit (Qiagen, Hilden, Germany). RNA (1 μg) was reverse transcribed using SuperScript III First-Strand Synthesis SuperMix (Life Technologies, Carlsbad, CA, USA) and obtained cDNA was used for qRT-PCR at the TaqMan 7900HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) utilizing TaqMan Fast Advanced Master Mix (Life Technologies). Commercial primers used in this study are listed in Additional file 2: Materials and methods. RNA-seq study: cells were treated for 8 h (P-TEFb—0.05 μM, OTX015—1 μM), 24 h (BAY-155—2 μM, Brequinar—2 μM, DMSO—0.1%) and 96 h (EPZ-5676—3 μM, DMSO—0.1%) prior to RNA extraction using RNeasy-Plus Mini kit (Qiagen). Obtained RNA was used for library preparation (Illumina, San Diego, CA, USA. TruSeq Stranded mRNA Kit) and obtained libraries were sequenced (Illumina, HiSeq2500 HTv4, SR, dual-indexing, 50 cycles).