biostudies-arrayexpressGozde BuyukkahramanHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13347Single cell RNA sequencing (scRNA-seq) of GM12878 cells upon G1/S blocker or control (DMSO) and Sendai virus infection.biostudies-arrayexpressNucleic Acid Extraction - RNA extraction from each cell was performed according to 10x Chromium Single Cell 3' protocol.Sample Collection - When cells are 80% confluent, aphidicolin or DMSO at 1uM concentration was added to the media and incubated for 12 hours at 37C. Sendai Virus or media was added to the media and incubated for additional 12 hours at 37C. Cells were collected at the end of 24h incubation.Sample Treatment - When cells are 80% confluent, aphidicolin or DMSO at 1uM concentration was added to the media and incubated for 12 hours at 37C. Sendai Virus or media was added to the media and incubated for 12 hours at 37C.Library Construction - Library construction was performed according to 10x Chromium Single Cell 3' protocol.Sequencing - Pair end sequencing was performed per instructions from the manufacturer (Illumina). 50 bases were sequenced.Growth Protocol - GM12878 cells were cultured with RPMI media supplemented with 10% FBS 37C with 5% CO2.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw count matrix was provided. No normalization was performed.Sequence Alignment - fastq file to count matrix was done with CellRanger count command with default settings.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2000Interferons (IFNs) have various roles in antiviral immunity, including curbing the immune system to prevent tissue damage and stimulating adaptive immunity. Due to its protective and destructive properties, IFN expression is tightly regulated. In contrast to its tight regulatory control, IFN expression is highly heterogeneous across many cell types upon pathogenic stimulus. The basis for this heterogenous IFN expression remains incompletely understood. Using single cell RNA-sequencing upon viral infection, we found that interferon expression is upregulated specifically in the late G1 phase of the cell cycle, and cell synchronization at the G1/S boundary boosts interferon expression. Furthermore, cell cycle arrest without any additional stimulus is sufficient to upregulate interferons and hundreds of other inflammatory response genes. Interferon upregulation at the G1/S boundary is cell type specific and not observed in non-immune cell types. Finally, we use ATAC-seq to identify potential transcription factors orchestrating this response. Together, these results uncover the cell cycle as a critical regulator of IFN expression in immune cells.RNA-seq of coding RNA from single cellsHomo sapiensG1/S Boundary Activates Interferon and Inflammatory Response GenesTae Hoon KimGozde BuyukkahramanBuyukkahraman, G. and Kim, T.H.falseSingle cell RNA-seq of human GM12878 cells infected with Sendai virus and treated with aphidicolin against untreated controlSingle cell RNA sequencing (scRNA-seq) of GM12878 cells upon G1/S blocker or control (DMSO) and Sendai virus infection.2025-08-27T00:00:00Z2024-07-30T20:00:30.806Z2023-09-18T13:17:56.756ZE-MTAB-13347ERP151266EFO_0002944EFO_0004170EFO_0003789EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_000396910.1101/2023.08.24.554683