{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Tina Karagyozova"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14417"],"description":["We 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth 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 Curie"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_title":["HIRA-dependent provision of histone H3.3 in active chromatin ensures genome compartmentalisation"],"pubmed_authors":["Tina Karagyozova","Jean-Pierre Quivy","Marc Marti-Renom","Alberto Gatto","Tina Karagyozova, Alberto Gatto, Audrey Forest, Jean-Pierre Quivy, Marc Marti-Renom, Leonid Mirny, Geneviève Almouzni","Audrey Forest","Leonid Mirny","Geneviève Almouzni"],"additional_accession":[]},"is_claimable":false,"name":"Total RNA-seq in WT and HIRA KO HeLa cells","description":"We 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.","dates":{"release":"2025-08-07T00:00:00Z","modification":"2025-08-08T00:02:08.174Z","creation":"2024-09-04T21:29:09.714Z"},"accession":"E-MTAB-14417","cross_references":{"ENA":["ERP163838"],"Biostudies":["E-MTAB-14419","E-MTAB-14416","E-MTAB-14415","E-MTAB-10619"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0004184"],"doi":["10.1101/2024.08.27.609896"]}}