biostudies-arrayexpressBibiana FerreiraHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16439Comparison of RNA levels between UACC-62 melanoma cell line and UACC-62 TRIB2 CRISPR/Cas9 knock-out cells. Three biological replicates of each cell line were analysed by bulk RNA-seq.biostudies-arrayexpressLibrary Construction - Total RNA (50 ng) was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification.Nucleic Acid Extraction - RNA was extracted using the Macherey-Nagel NucleoSpin RNA kit according to the manufacturer´s protocol.Sequencing - Libraries were sequenced on a HiSeq4000 (Illumina) to generate 60 bases single reads. FastQ files for each sample were obtained using bcl2fastq 2.20 Software software (Illumina).Sample Collection - Cells pellets were collected using Trypsin/EDTA centrifuged and pellet was immediately forenOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - RNA-seq reads were processed using the nf-core/rnaseq pipeline (Workflow: nf-core/rnaseq: v3.21.0-g9738a2d; Nextflow: 25.04.8). Briefly, raw reads were quality-checked and adapter-trimmed, then aligned to the human reference genome (GRCh38.primary_assembly) using STAR. Gene-level read counts were generated based on the corresponding genome annotation (gencode.v41.primary_assembly). Default nf-core/rnaseq parameters were used.Data Transformation - Gene-level raw counts and TPM values were generated using the nf-core/rnaseq pipeline. Transcript-level estimates were summarised to gene-level using tximport. TPM values were calculated using standard length and library-size normalisation. No further transformation was applied.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 4000RNA-seq of coding RNAHomo sapiensBibiana FerreirafalseRNA-seq of human melanoma cell line UACC-62 parental and TRIB2 knock-out clonesComparison of RNA levels between UACC-62 melanoma cell line and UACC-62 TRIB2 CRISPR/Cas9 knock-out cells. Three biological replicates of each cell line were analysed by bulk RNA-seq.2026-04-27T00:00:00Z2026-04-27T12:14:10.253Z2025-12-19T17:09:25.596ZE-MTAB-16439ERP186853EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184