{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Veronica Busa"],"organism":["Heterocephalus glaber"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13538"],"description":["Mice are cancer-prone, whereas naked mole-rats are cancer-resistant. Because fibroblasts support the development of skin cancer, SCC25 cells were co-cultured with either mouse or naked-mole rat cells and the difference in SCC25 cells grown alone or with the different types of fibroblasts were compared. Cells were grown together for two days, then FACS-sorted and bulk-sequenced separately."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Pooled libraries were sequenced in one P3 flow cell on a Illumina  Illumina NextSeq2000 sequencer using a 100 bp paired-end read protocol.","Library Construction - RNA-sequencing libraries prepared using Illumina stranded total RNA Prep, Ligation with RiboZero Plus (Illimuna) following manufacturer's instructions.","Nucleic Acid Extraction - Total RNA was extracted by adding 800 µl TRIzol reagent (Life Technologies). Total RNA samples were DNased treated using Turbo DNase (Life Technologies).","Sample Collection - For two-dimensional co-culture, SCC25-tdTomato cells were seeded in a 1:1 ratio with mouse or naked mole-rat fibroblasts in DMEM/F12 medium (11320-032, Life Technologies) supplemented with 0.05% FBS (Life Technologies), 400 ng/ml hydrocortisone (Santa Cruz Biotechnology) and 1% Penicillin-Streptomycin (PEST) and cultured in a 37°C incubator with 5% CO2. After 48 hours SCC25-tdTomato and fibroblasts were separated using FACS sorting (E-cadherin-APC staining to separate SCC25 from fibroblasts (TdTom &E-cadherin-). Approximately 50,000-100,000 cells were sorted of each cell type from each condition."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Each sample was aligned to its corresponding species' genome (GRCh38, GRCm10, HetGla_female) via STAR 2.7.10a","Data Transformation - Ortholog lists were derived from Ensembl and counts were taken from STAR output. Reads for many-to-one orthologs were summed. Counts were log-transformed and genes with no expression were excluded for downstream analysis."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Heterocephalus glaber"],"pubmed_authors":["Veronica Busa","Mikaela Behm"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA-seq of co-cultured SCC25 and mouse or naked mole-rat fibroblasts","description":"Mice are cancer-prone, whereas naked mole-rats are cancer-resistant. Because fibroblasts support the development of skin cancer, SCC25 cells were co-cultured with either mouse or naked-mole rat cells and the difference in SCC25 cells grown alone or with the different types of fibroblasts were compared. Cells were grown together for two days, then FACS-sorted and bulk-sequenced separately.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2025-12-31T02:02:13.217Z","creation":"2023-11-16T19:19:39.038Z"},"accession":"E-MTAB-13538","cross_references":{"ENA":["ERP154468"],"Biostudies":["E-MTAB-12459","E-MTAB-12454","E-MTAB-12456","E-MTAB-12461","E-MTAB-12451"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}