{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Markus Riessland"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15005"],"description":["Cells were treated chronically for 7 days with a sub-lethal dose (100uM) of 5-Bromodeoxyuridine (BrdU) to trigger DNA damage-induced cellular senescence. Senescence phenotype was confirmed with multiple cellular markers such as SA-b-Gal staining, lamin B1 downregulation, increased size of nucleus, metabolic shift, etc. Total RNA was isolated after day 7 of treatment (3 samples DMSO, 3 samples BrdU) and RNA-seq was performed. Cell lines used: HBEC5i: endothelial cells, HMC3: microglia, HOG: Oligodendrocytes, SKNMC: neuronal cells, SVGA: astrocytes"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - After the completion of the treatment time,  total RNA was isolated from cell culture","Nucleic Acid Extraction - To isolate and purify the RNA, RNeasy plus (mini), Qiagen kit was used according to the manufacturer's protocol.","Library Construction - The library preparation was performed by using an Illumina seq library kit (performed by Azenta)","Sequencing - Illumina seq, 150bp, ~350M PE reads (performed by Azenta)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Markus Riessland"],"additional_accession":[]},"is_claimable":false,"name":"Cell lines treated with BrdU against DMSO controls (DNA damage-induced senescence)","description":"Cells were treated chronically for 7 days with a sub-lethal dose (100uM) of 5-Bromodeoxyuridine (BrdU) to trigger DNA damage-induced cellular senescence. Senescence phenotype was confirmed with multiple cellular markers such as SA-b-Gal staining, lamin B1 downregulation, increased size of nucleus, metabolic shift, etc. Total RNA was isolated after day 7 of treatment (3 samples DMSO, 3 samples BrdU) and RNA-seq was performed. Cell lines used: HBEC5i: endothelial cells, HMC3: microglia, HOG: Oligodendrocytes, SKNMC: neuronal cells, SVGA: astrocytes","dates":{"release":"2025-10-15T00:00:00Z","modification":"2025-10-15T17:42:43.104Z","creation":"2025-04-09T12:25:07.7Z"},"accession":"E-MTAB-15005","cross_references":{"ENA":["ERP171396"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}