biostudies-arrayexpressJelena BudimirCricetulus griseushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15733UV-treated cells were stained in green and seeded in density-matched monoculture with equally treated cells or in co-culture with untreated cells. The cultures were kept for 12 h prior to cell sorting and RNA isolation for bulk RNA sequencing. We wanted to compare transcriptional signatures of the UV-treated cells incubated in co-culture with the control set kept in monocultre, because the two cellular populations dispalyed morphologically different response to UV.biostudies-arrayexpressSample Collection - The cells were sorted based on GFP fluorescence directly into RLT buffer to lyse them and prevent RNA degradation.Sequencing - Sequencing was performed on high-throughput sequencing platform Illumina A01426.Sample Treatment - Cells stained with cytoplasmic dye in green were treated with a combination of UV-C and UV-C light of 0.15 J/cm2 and seede in monoculture with eqally treated cells or in coculture with untreated cells. After 12 hours incubation, cells were sorted based on the green fluorescence.Nucleic Acid Extraction - Total cellular RNA was isolated using Qiagen RNEasy Mini kit, and DNA was removed by the addition of DNase I (New England Biolabs).Growth Protocol - V79 chinese hamster pulmonary fibroblast cells were cultured in DMEM supplemented with 10 % fetal bovine serum (FBS) in humidified atmosphere with 5 % CO2 at 37 °C.Library Construction - Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Reference genome and gene model annotation files were downloaded from genome website (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/223/135/GCF_000223135.1_CriGri_1.0/GCF_000223135.1_CriGri_1.0_genomic.gff.gz ). 2 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Processed data file is .xlsx file which includes gene counts for each sample.Data Transformation - Differential gene expression analysis was performed using the DESeq2 R package v1.47.0 (Love et al., 2014). Raw counts were first pre-filtered to remove genes with less than 10 reads in total, normalized with DESeq2 default parameters and transformed using variance stabilizing transformation (VST). To examine sample clustering, principal component analysis (PCA) was performed on the normalized counts. To correctly measure the effect of various test conditions, samples were modelled to control for batch differences and other technical differences arising from the experimental design. For effect size shrinkage, the “ashr” method was used which implements an empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation (ashr R package v2.2-63). For further downstream analysis, differentially expressed genes (DEGs) were defined with FDR adjusted p-value < 0.05 and fold change > 2 for upregulated genes or < 0.5 for downregulated genes.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsQiagen RNEasy Mini kiNAIllumina NovaSeq 6000poly-T oligo-attached magnetic beadsBD FACSAriaIIu cell sorterRNA-seq of coding RNACricetulus griseusContact-dependent regulation of UV-B/C-induced cell fate by neighboring intact cellsJelena BudimirJelena Budimir, Nikola Pavlović, Andrea Gelemanović, Vanda Juranić-Lisnić, Swetlana Sperling, Milena Ninković, Miroslav Radman, Katarina TrajkovicfalseRNA-seq experiment of V79 cells treated with UV light and incubated either in monoculture or coculture with untreated cellsUV-treated cells were stained in green and seeded in density-matched monoculture with equally treated cells or in co-culture with untreated cells. The cultures were kept for 12 h prior to cell sorting and RNA isolation for bulk RNA sequencing. We wanted to compare transcriptional signatures of the UV-treated cells incubated in co-culture with the control set kept in monocultre, because the two cellular populations dispalyed morphologically different response to UV.2026-03-09T00:00:00Z2026-03-22T10:40:45.61Z2025-10-15T14:11:29.69ZE-MTAB-15733ERP182238EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969