{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Patrick Nylund"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13813"],"description":["Here we investigated the molecular response DNMT- and G9a inhibition in multiple myeloma."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Sequencing libraries were prepared from 100ng total RNA using the Illumina Stranded Total RNA library preparation kit with Ribo-Zero Plus treatment (cat# 20040525/20040529, Illumina Inc.)","Sample Collection - INA-6, OPM2 and KMS-28PE were selected for combinatorial treatment response analysis. INA-6 and KMS28-PE cells were seeded at 100.000 cells/ml while OPM2 cells were seeded at 200.000 cells/mL 24h prior treatment with H2O and DMSO (Sigma-Aldrich) or 50nM of AZA (Abcam) and 5μM or 10μM of A366 (Tocris Bio-techne). AZA treatment was administrated every day while A366 treatment was added every 3 days. Media and reagent refreshment was performed every 3 days. All experiments were performed in three independent cell batches per cell line.","Nucleic Acid Extraction - RNA was extracted using the RNeasy Micro Kit (Qiagen; Hilden; Germany #74004) as described by the manufacturer.","Sequencing - Paired-end 150bp read length, NovaSeq 6000 system, S4 flowcell and v1.5 sequencing chemistry."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The sequencing data from the combinatorial treated INA-6, KMS-28PE and OPM2 MM cell lines were analysed using the nf-core RNAseq pipeline (https://doi.org/10.5281/zenodo.3503887) in version 3.4, utilizing default parameters for paired-end analysis. Differential expression analysis was done by DESeq2 workflow as described: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_authors":["Patrick Nylund","Berta Garrido-Zabala"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq experiment of multiple myeloma cells under different treatment conditions against epigenetic modifiers","description":"Here we investigated the molecular response DNMT- and G9a inhibition in multiple myeloma.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2025-12-31T02:02:13.02Z","creation":"2024-02-28T21:19:02.117Z"},"accession":"E-MTAB-13813","cross_references":{"ENA":["ERP157492"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0003816","EFO_0004184"]}}