biostudies-arrayexpressNinela Miriama VainselbaumaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16509MDA-MB-231 breast cancer cells were treated with 100 nM doxorubicin for 24h and observed over time in order to elucidate the biological processes of phenotypical adaptation involved in chemoresistance development and identify potential novel targets for future combination therapies.biostudies-arrayexpressSequencing - The DNBSEQ-G400 sequencing platform (MGI, China) was used for sequencing the libraries. The RNA concentrations after extraction, dsDNA concentrations after amplification, and ssDNA concentrations after multiplexing were determined using the appropriate Qubit assays: Qubit™ RNA HS Assay Kit, Qubit™ dsDNA HS Assay, Qubit™ ssDNA HS Assay Kit, and Qubit® 2.0 Fluorometer (Thermo Fisher Scientific, Rockford, IL, USA). The fragment size after amplification was determined using a high sensitivity DNA kit and Agilent 2100 bioanalyzer (Agilent Technologies, USA).Sample Collection - The human melanoma SK-MEL-28 cell line was obtained from the ATCC (The American Type Culture Collection, Manassas, VA, USA). Samples for RNA-seq were taken at days 5, 8, 16 and 22 after treatment, along with nontreated controls.Library Construction - Transcriptome library preparation was performed using the MGIEasy RNA Directional Library Prep Kit (MGI, China). Veriti 96 Well Thermal Cycler (Applied Biosystems) was used to carry out all reactions and incubations as intended in the library preparation protocol. RNA enrichment was performed by depleting rRNA with MGIEasy rRNA Depletion Kit (MGI, China). Work continued accordingly with instructions to the 250bp insert size.Nucleic Acid Extraction - RNA isolation was performed using AllPrep DNA/RNA/miRNA Universal Kit (50) (Qiagen, Germany). RNA quality was determined using RNA 6000 Pico Kit and Agilent 2100 bioanalyzer (Agilent Technologies, USA).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - The RNA-seq reads were trimmed of adapters with Cutadapt and pseudo-aligned to the GRCh38.p13 human transcriptome reference with Salmon.Data Transformation - Transcript-level quantification values from Salmon were converted to gene-level abundance values in length-scaled TPM units for each sample, using tximport.UnknownTranscriptomicsGenomicsProteomicsDNBSEQ-G400RNA-seq of coding RNAHomo sapiensNinela Miriama VainselbaumafalseTime-series RNA-seq reads of MDA-MB-231 cells treated with 100nM doxorubicinMDA-MB-231 breast cancer cells were treated with 100 nM doxorubicin for 24h and observed over time in order to elucidate the biological processes of phenotypical adaptation involved in chemoresistance development and identify potential novel targets for future combination therapies.2026-01-12T00:00:00Z2026-01-12T02:02:17.23Z2026-01-02T15:57:40.747ZE-MTAB-16509ERP187228EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184