biostudies-arrayexpressVeronica BusaHeterocephalus glaberhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13538Mice 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.biostudies-arrayexpressSequencing - 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.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Each sample was aligned to its corresponding species' genome (GRCh38, GRCm10, HetGla_female) via STAR 2.7.10aData 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.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000RNA-seq of coding RNAHeterocephalus glaberVeronica BusaMikaela BehmfalseBulk RNA-seq of co-cultured SCC25 and mouse or naked mole-rat fibroblastsMice 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.2025-12-31T00:00:00Z2025-12-31T02:02:13.217Z2023-11-16T19:19:39.038ZE-MTAB-13538ERP154468E-MTAB-12459E-MTAB-12454E-MTAB-12456E-MTAB-12461E-MTAB-12451EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184