{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Charlène Renaud-Pageot"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15582"],"description":["CENP-A, the centromeric histone H3 variant, is essential for the proper segregation of human chromosomes to daughter cells. High CENP-A expression leads to the misincorporation of CENP-A in non-centromeric chromatin and can promote an epithelial-mesenchymal transition (EMT).  Here, we explored how CENP-A could promote EMT, considering both its impact on transcription and chromatin structure. For this, we used a MCF10-2A TetOn-CENPA-FLAG-HA cell line where high CENP-A expression can be induced by Doxycycline (Dox) treatment. This cell line is p53-defective (transduction with a dominant-negative (DN) p53 vector). Upon CENP-A overexpression, these cells progressively accumulate mesenchymal states. For the same nuclei, we jointly profiled single-nucleus RNA (snRNA) and single-nucleus ATAC (snATAC) data using 10X Multiome at days 10 and 24 (prior and after the mesenchymal states accumulation). In order to profile changes in transcription and cell states, we compared cells expressing either basal CENP-A levels (non-induced, control with no Dox), or high CENP-A levels (induced with 10 ng/ml Dox)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Library construction by Active Motif services using the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent kit. Steps included nuclei transposition, generation of Gel Beads in Emulsion (GEMs) and 10X barcoding, cleanup, pre-amplification of ATAC DNA and cDNA, amplification with P5 and P7 adapters, Illumina sequencing.","Sequencing - Sequenced on an Illumina NovaSeq 6000 according to 10x Genomics recommendations.","Nucleic Acid Extraction - Single-nuclei suspensions prepared using 10X Nuclei Isolation protocols.","Sample Collection - MCF-10-2A TetOn-CENPA-FLAG-HA cells stably expressing a dominant-negative p53 vector (p53-DN) were cultured for 24 days in the absence (no Dox) or presence of Dox (10 ng/mL) to induce basal or high CENP-A expression, respectively. Culture medium (+/- Dox) was renewed every 2-3 days. We harvested cells at days 10 and 24 post-induction and prepared 4 million cells/mL in ice-cold cryopreservation medium (50% fetal bovine serum, 40% growth medium and 10% dimethyl sulfoxide)."],"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":["single nucleus RNA sequencing"],"species":["Homo sapiens"],"pubmed_title":["Non-centromeric CENP-A epigenetically regulates epithelial-mesenchymal plasticity and heterogeneity in human cells"],"pubmed_authors":["Charlène Renaud-Pageot, Daniele Capocefalo, Sébastien Lemaire, Audrey Forest, Laura Cantini, Geneviève Almouzni","Charlène Renaud-Pageot"],"additional_accession":[]},"is_claimable":false,"name":"Multiome snRNA + snATAC on MCF10-2A cells to study how high CENP-A levels promote EMT","description":"CENP-A, the centromeric histone H3 variant, is essential for the proper segregation of human chromosomes to daughter cells. High CENP-A expression leads to the misincorporation of CENP-A in non-centromeric chromatin and can promote an epithelial-mesenchymal transition (EMT).  Here, we explored how CENP-A could promote EMT, considering both its impact on transcription and chromatin structure. For this, we used a MCF10-2A TetOn-CENPA-FLAG-HA cell line where high CENP-A expression can be induced by Doxycycline (Dox) treatment. This cell line is p53-defective (transduction with a dominant-negative (DN) p53 vector). Upon CENP-A overexpression, these cells progressively accumulate mesenchymal states. For the same nuclei, we jointly profiled single-nucleus RNA (snRNA) and single-nucleus ATAC (snATAC) data using 10X Multiome at days 10 and 24 (prior and after the mesenchymal states accumulation). In order to profile changes in transcription and cell states, we compared cells expressing either basal CENP-A levels (non-induced, control with no Dox), or high CENP-A levels (induced with 10 ng/ml Dox).","dates":{"release":"2026-04-24T00:00:00Z","modification":"2026-04-24T16:03:20.706Z","creation":"2025-09-08T15:27:57.096Z"},"accession":"E-MTAB-15582","cross_references":{"ENA":["ERP179785"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009809","EFO_0005518","EFO_0004184"]}}