GSM9020048: MCF7-DOXO-2-1, bulkRNAseq; Homo sapiens; RNA-Seq
Total RNA was isolated from MCF-7 cells treated with either vehicle control (0.1% DMSO) or 250 nM doxorubicin for 72 hours using the RNeasy Mini Kit (Qiagen, Santa Clarita, CA) on an automated QIAcube extractor (Qiagen, Santa Clarita, CA), following the manufacturer's instructions. RNA-seq libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero™ Plus kit (Illumina, San Diego, CA, USA, Cat# 20040525), following the manufacturer's protocol. Libraries were generated from 100 ng of total RNA, which was initially depleted of abundant ribosomal RNA (rRNA). The remaining RNA was then reverse transcribed into cDNA, followed by ligation and amplification steps to add adapters for clustering and sequencing. The final library concentrations were measured using Qubit 4, and quality control was performed with the TapeStation 4200. All libraries were purified and diluted to a starting concentration of 0.5 nM. The pooled libraries were sequenced at 2×75 base pairs on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) using a NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles).