biostudies-arrayexpressTina KaragyozovaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14431We performed Hi-C in asynchronous HeLa cells that knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene transfected with HIRA-YFP (HIRA) or YFP only (control) plasmid.biostudies-arrayexpressLibrary Construction - We sonicated DNA using Covaris E220 Evolution (100μL sample, 7 degrees C, peak incident power: 105W, duty factor: 5%, cycles/burst: 200 for 100s), and fragmented DNA was size selected using AMPure XP beads. We verified that the mean size of selected DNA was 400bp using Tapestation. After biotin enrichment, we performed library preparation using the KAPA HyperPrep kit, following the modified protocol described in the Arima Hi-C+ kit instructions. After ligation of Illumina TruSeq sequencing adaptors, we performed Arima QC2 (library quantification) to determine the number of amplification cycles for the library PCR using the KAPA Library Quantification Sample kit following the manufacturer’s instructions.Sample Collection - We performed Hi-C using the Arima Hi-C+ kit following the manufacturer’s instructions. Briefly, 3-5 million asynchronous HeLa cells per condition were fixed in 4% formaldehyde for 10min before quenching the reaction with Stop Solution 1. Fixed cells were washed in PBS and snap-frozen in liquid nitrogen at 1 million cell aliquots.Nucleic Acid Extraction - We performed cell and nuclear lysis, restriction enzyme digestion, end repair, biotinylation, ligation and decrosslinking as per manufacturer’s instructions and proximally ligated DNA was isolated using AMPure XP beads. Arima QC1 was performed and was successful for all samples.Sequencing - Amplified libraries were sequenced on Illumina NovaSeq 6000 (PE100) at the NGS (Next-Generation Sequencing) platform at Institut Curie.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000Hi-CHomo sapiensHIRA defines early replication initiation zones independently of their genome compartmentTina KaragyozovaJean-Pierre QuivyMarc Marti-RenomAlberto GattoTina Karagyozova, Alberto Gatto, Audrey Forest, Jean-Pierre Quivy, Marc Marti-Renom, Leonid Mirny, Geneviève AlmouzniAudrey ForestLeonid MirnyGeneviève AlmouznifalseHi-C to compare 3D genome organisation in HIRA KO HeLa cells rescued with HIRAWe performed Hi-C in asynchronous HeLa cells that knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene transfected with HIRA-YFP (HIRA) or YFP only (control) plasmid.2025-08-07T00:00:00Z2025-08-08T00:01:36.51Z2024-09-06T15:49:14.711ZE-MTAB-14431ERP163937E-MTAB-14433EFO_0007693EFO_0002944EFO_0004170EFO_0005518EFO_000418410.1101/2024.08.29.610220