{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Carl MANN"],"organism":["Homo sapiens"],"software":["Salmon and tximeta","EdgeR and Limma"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16030"],"description":["Transcriptomic analysis of inflammatory gene expression in a human mammary fibroblast cell line in proliferation and IR-induced senescence, with and without IL1-alpha treatment (10 pg/ml for 24 hours). Cells were induced into senescence by irradiation with 40 Gy of 120 kV X-rays and then incubated 9 days before treating with IL1-alpha."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Paired-End 42 nucleotides in an Illumina NextSeq 500 sequencer.","Growth Protocol - DMEM + glutamine + pyruvate + pen/strep in 5% O2 + 5% CO2 incubator.","Nucleic Acid Extraction - RNA was extracted with the Macherey-Nagel Nucleospin RNA Plus.","Sample Collection - Cell monolayers were trypsinized, neutralized with medium, washed with PBS, and centrifuged. Washed cell pellets were resuspended in Macherey-Nagel Nucleospin RNA Plus Lysis Buffer.","Library Construction - NEBNext Ultra II Directional RNA Library Kit with PolyA RNA selection","Sample Treatment - Proliferating cells were treated with 10 pg/ml Interleukin-alpha (Sigma I2778)for 24 hours. M168 cells were induced into senescence by irradiating with 40 Gy of 120 KV X-rays produced by a Faxitron 43855D generator. Cells were incubated for 10 days post irradiation before harvesting for RNA isolation. For IL1-alpha treatment of irradiated cells, the cells were irradiated with 40 Gy of 120 KV X-rays as above and cells were incubated for 9 days and then treated for 24 hours with 10 pg/ml of IL1-alpha (Sigma I2778)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Data were normalized with EdgeR and Limma voom","Sequence Alignment - Fastq sequences were mappled to the human transcriptome using the Salmon transcriptome alignment software."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 550"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Carl MANN"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of a human mammary fibroblast cell line in proliferation and IR-induced senescence with and without IL1-alpha treatment.","description":"Transcriptomic analysis of inflammatory gene expression in a human mammary fibroblast cell line in proliferation and IR-induced senescence, with and without IL1-alpha treatment (10 pg/ml for 24 hours). Cells were induced into senescence by irradiation with 40 Gy of 120 kV X-rays and then incubated 9 days before treating with IL1-alpha.","dates":{"release":"2026-01-01T00:00:00Z","modification":"2026-01-02T02:03:17.382Z","creation":"2025-11-06T12:48:18.069Z"},"accession":"E-MTAB-16030","cross_references":{"ENA":["ERP183775"],"Biostudies":["E-MTAB-14265","E-MTAB-14201"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}