GSM8735773: V1_K562BCO_Untreated_A25_S5; Homo sapiens; RNA-Seq
For RNA sequencing total RNA was extracted from cells, using the RNeasy Mini Kit from Qiagen (Venlo, The Netherlands) according to the manufacturer's recommendations. RNA samples were qualified by automated gel electrophoresis on the 2200 TapeStation System (Agilent Technologies). Using KAPA RNA HyperPrep kit with riboErase (HMR) from Roche Sequencing and Life Sciences, cDNAs were synthesized from fragmented RNA and the sequences library were generated, according to the manufacturer's recommendations. These libraries were then sequenced on an Illumina NextSeq500 using standard settings and the single-end reads obtained from treated cells were analyzed with Strand Avadis NGS (v3.0) software (Strand Life Sciences Pvt. Ltd). The STAR aligner was used in two-pass mode with default settings to map the obtained paired-end reads from treated cells to the hg38 reference genome. Using the DESeq2 package, the data was normalized and differentially expressed genes (DEGs) were found. Genes with an adjusted p-value < 0.05 and log2FoldChanges > < 0.585 were found to be differentially expressed and were used in further analysis.