biostudies-arrayexpressGozde BuyukkahramanHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13339ATAC-seq of human GM12878 cells to detect chromatin accessibility changes upon G1/S arrest (aphidicolin treated samples) and /or infection (Sendai virus) compared to control.biostudies-arrayexpressNucleic Acid Extraction - Protocol was taken from different studies (Buenrostro, Giresi et al. 2013, Buenrostro, Wu et al. 2015, Corces, Trevino et al. 2017, Brunton, Garner et al. 2020) and solutions were prepared according to (Corces, Trevino et al. 2017). Briefly, 60K cells were sorted and lysed in 50 μL cold lysis buffer on ice for 3 min. Lysis was quenched by adding 1 mL of wash buffer. Cells were centrifuged at 500xg for 10 min at 4 °C and supernatant (cytoplasm) was discarded. Nuclei were gently resuspended with transposition mix and incubated at 37 °C for 30 minutes at 1,000 rpm. DNA was purified using DNA Clean & Concentrator-5 (Zymo Research, D4013) according to the manufacturer’s instructions.Sample Collection - At the end of 24 hours, cells death was measured with PE Annexin-V (BD Biosciences) according to manufacturer’s instructions. Cells were stained with 7-AAD viability staining solution (BD Biosciences) and 60,000 live cells per condition were sorted by BDAria Fusion and FlowJo software.Library Construction - Protocol was taken from different studies (Buenrostro, Giresi et al. 2013, Buenrostro, Wu et al. 2015, Corces, Trevino et al. 2017, Brunton, Garner et al. 2020) and solutions were prepared according to (Corces, Trevino et al. 2017). Briefly, 60K cells were sorted and lysed in 50 μL cold lysis buffer on ice for 3 min. Lysis was quenched by adding 1 mL of wash buffer. Cells were centrifuged at 500xg for 10 min at 4 °C and supernatant (cytoplasm) was discarded. Nuclei were gently resuspended with transposition mix and incubated at 37 °C for 30 minutes at 1,000 rpm. DNA was purified using DNA Clean & Concentrator-5 (Zymo Research, D4013) according to the manufacturer’s instructions. PCR amplification (library generation) was performed according to the previous study (Brunton, Garner et al. 2020). Library was purified using AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions.Sequencing - To assess the library quality, each sample was run on an Agilent High Sensitivity DNA Bioanalysis chip following manufacturer’s instructions. DNA concentrations were measured by Qubit™ dsDNA HS Assay Kit (Invitrogen, Catalog Numbers Q32851, Q32854) following manufacturer’s instructions. 50 bp paired-end sequencing was performed by Illumina Nextseq 2000.Growth Protocol - GM12878 cells were cultured with RPMI media supplemented with 10% FBS 37C with 5% CO2Sample Treatment - When cells are 80% confluent, 1 uM of aphidicolin was added to the media and incubated for 12 hours at 37C. Sendai Virus or media was added to the media and incubated for and additional of 12 hours at 37C.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw count matrix was provided. No normalization was performed.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.ATAC-seqHomo sapiensG1/S Boundary Activates Interferon and Inflammatory Response GenesTae Hoon KimGozde BuyukkahramanBuyukkahraman, G. and Kim, T.H.falseATAC-seq of human GM12878 cells treated with aphidicolin and infected with Sendai virus against untreated controlATAC-seq of human GM12878 cells to detect chromatin accessibility changes upon G1/S arrest (aphidicolin treated samples) and /or infection (Sendai virus) compared to control.2025-08-27T00:00:00Z2024-07-30T20:00:55.388Z2023-09-11T21:06:10.36ZE-MTAB-13339ERP151078EFO_0002944EFO_0007045EFO_0004170EFO_0003789EFO_0005518EFO_0003816EFO_0004184EFO_000396910.1101/2023.08.24.554683