biostudies-arrayexpressGinés Luengo-GilHomo sapiensKallisto for WindowsDegust online server (https://degust.erc.monash.edu/)Manual protocolNextSeq 1000/2000 Control Software Suitehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15351Imipramine, a tricyclic antidepressant, has demonstrated antitumoral properties in various preclinical studies (both in vitro and in vivo), although it is not currently approved for cancer treatment. The aim of this experiment is to investigate the transcriptomic changes associated with imipramine treatment (24, 48 and 72 h) in vitro in luminal and triple-negative breast cancer cell models. RNA-seq (raw data), 5 biological replicates per condition.biostudies-arrayexpressLibrary Construction - RNA sequencing was performed at the Genomics Department of the Institute of Biomedicine in Murcia (IMIB), using the Illumina NextSeq 2000 platform. A total of 1000 ng of RNA per sample was used for library preparation using the Illumina Stranded mRNA Prep Kit following the manufacturer's instructions. Briefly, oligo(dT) magnetic beads were used to purify and capture mRNA molecules containing polyA tails. Purified mRNA was fragmented and reverse-transcribed into the first strand of complementary DNA (cDNA) using random primers. In the second-strand cDNA synthesis step, dUTP replaces dTTP to achieve strand specificity. In the final steps, adenine (A) and thymine (T) bases are added to the ends of the fragments and adapters are attached. The resulting products were purified and selectively amplified for sequencing using the Illumina system.Sequencing - The generated libraries were sequenced on the NextSeq 2000 platform (Illumina), producing paired-end reads using the NextSeq 2000 P3 Reagent cartridge (200-cycle).Sample Collection - Both cell lines were seeded in 6-well plates at a density of 100,000 cells/well per sextuplicate and treated with 20 µM of imipramine. Cells were collected after 24, 48, and 72 h (with or without treatment) using 800 µL of TRIzol™ Reagent (Thermo Fisher Scientific).Nucleic Acid Extraction - Total RNA was extracted using the Direct-zol™ RNA MiniPrep kit (Zymo Research, USA, Cat# R2050).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Pseudoalignment and quantification of transcript abundances from bulk RNA-Seq data were performed using Kallisto (https://pachterlab.github.io/kallisto/).Data Transformation - RNA-seq exploration, analysis and visualisation were performed using Degust (https://degust.erc.monash.edu/). Normalization of gene expression levels was performed using the CPM (Counts Per Million) method, which adjusts for differences in sequencing depth between samples.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsManual protocolMSI GP76 Leopard 10UE-060ES Intel Core i7-10870H/16GB/1TB SSD/RTX 3060/17.3\NextSeq 2000RNA-seq of coding RNAHomo sapiensCharacterization and Prognostic Impact of Fascin Expression in the Tumor Microenvironment of Triple-Negative Breast Cancer: Clues for a Tailored Therapy.Ginés Luengo-GilPablo Conesa-ZamoraPérez-Parra D, Postigo-Corrales F, Cruz AF, Sánchez-Espinosa A, Acosta-Ortega J, Carrillo-Vicente R, López-Abellán MD, Conesa-Zamora P, Luengo-Gil G, Hurtado-López AM.falseRNA-seq analysis of human breast cancer cell lines MCF7 and MDA-MB-231 treated with imipramine compared to untreated controlsImipramine, a tricyclic antidepressant, has demonstrated antitumoral properties in various preclinical studies (both in vitro and in vivo), although it is not currently approved for cancer treatment. The aim of this experiment is to investigate the transcriptomic changes associated with imipramine treatment (24, 48 and 72 h) in vitro in luminal and triple-negative breast cancer cell models. RNA-seq (raw data), 5 biological replicates per condition.2026-04-09T00:00:00Z2026-04-09T13:36:32.42Z2025-07-09T15:28:43.01ZE-MTAB-15351publ-0-plgc-removableERP175152EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_000418410.1016/j.labinv.2025.104268