The RNA from the cell lines was extracted from the same passage of cells, which were chosen for DNA extraction (for RRBS), using a PureLink RNA mini kit (Invitrogen, Catalog #12183025). The total RNA was extracted according to the manufacturer's instructions. RNA purity was determined by measuring absorbance using a Nanodrop ND-1000 spectrophotometer (ThermoFisher Scientific, USA). RNA samples with an A260/A280 between 1.8 to 2.0 and A260/A230 close to 2.0 were chosen for downstream analysis. RNA concentration was determined using a Qubit RNA HS kit (Invitrogen, Catalog # Q32852) according to the manufacturer's instructions. RNA integrity was determined by an Agilent Bioanalyzer 2100 system and associated RNA 6000 Nano kit (Agilent, Catalog # 5067-1511). The RIN values of all the samples used for the RNASeq analysis were >=8.0. The library preparation was carried out by enrichment of poly-A tailed transcripts from the total RNA and the library type was strand-specific. A TrueSeq mRNA stranded library prep kit (Illumina, Catalog # RS-122-2101) was used for mRNA library preparation. Paired end sequencing of 125 bp was carried out in Illumina 2500 V4 sequencer.
GEO Accession
GSM4647729