biostudies-arrayexpressTina KaragyozovaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14417We performed total RNA-seq of G1/S-synchronised HeLa cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene.biostudies-arrayexpressGrowth Protocol - We used HeLa cells stably expressing H3.3-SNAP-HA or H3.1-SNAP-HA, and derived HIRA knockout cell lines (HIRA CRISPR/Cas9 KO) or HIRA wild-type control cells (GFP CRISPR/Cas9 KO) as described in Ray-Gallet et al. 2019. We cultured cells in DMEM complete medium with D-Glucose, L-Glutamine and Pyruvate, supplemented with 10% fetal calf serum, 100 U/mL Penicillin and 100 µg/mL Streptomycin. Cells were synchronized in G1/S via double thymidine block: subsequent exposure to 2 mM thymidine (16-18h), 24 µM 2-Deoxycytidine (6h) and 2 mM thymidine (18h).Nucleic Acid Extraction - Total RNA was extracted using the RNeasy Plus Mini Kit according to the manufacturer’s instructions. The total RNA was DNase treated by RNase-free DNase (QIAGEN, 79254) using manufacturer’s instructions. We measured the quantity of isolated RNA using Nanodrop and checked the quality by Tapestation.Sample Collection - Cells were collected by trypsinization (1 million cells per condition). To ensure cells remained in G1/S block, trypsin and PBS used for washes were supplemented with thymidine to 2mM final.Library Construction - We used 10 ng of total RNA for library preparation using TruSeq Stranded Total RNA kit.Sequencing - Libraries were sequenced on Illumina NovaSeq 6000 (PE100) by the NGS platform at Institut CurieOrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of total RNAHomo sapiensHIRA-dependent provision of histone H3.3 in active chromatin ensures genome compartmentalisationTina KaragyozovaJean-Pierre QuivyMarc Marti-RenomAlberto GattoTina Karagyozova, Alberto Gatto, Audrey Forest, Jean-Pierre Quivy, Marc Marti-Renom, Leonid Mirny, Geneviève AlmouzniAudrey ForestLeonid MirnyGeneviève AlmouznifalseTotal RNA-seq in WT and HIRA KO HeLa cellsWe performed total RNA-seq of G1/S-synchronised HeLa cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene.2025-08-07T00:00:00Z2025-08-08T00:02:08.174Z2024-09-04T21:29:09.714ZE-MTAB-14417ERP163838E-MTAB-14419E-MTAB-14416E-MTAB-14415E-MTAB-10619EFO_0002944EFO_0004170EFO_0009653EFO_0003789EFO_0005518EFO_000418410.1101/2024.08.27.609896