{"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-15579"],"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 its localization at EMT gene loci. 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. We performed bulk ChIP-seq experiments at the same time points as our transcriptomic data (day 10 and 24). In order to profile changes in CENP-A localization, 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 - Quality and concentration were assessed using a TapeStation 4200 (Agilent) and a Qubit 3.0 fluorometer (Invitrogen). Sequencing libraries were prepared with the Illumina TruSeq ChIP kit.","Sequencing - Sequencing was perfomred on the Illumina NovaSeq 6000 at the Institut Curie Next Generation Sequencing (NGS) platform.","Nucleic Acid Extraction - For each IP, 2-5 million cells were harvested and processed in aliquots of 1 million cells per tube by resuspending cell pellets in 100 µL ice-cold lysis buffer for a 4-min incubation at room temperature. We prepared antibody-coupled Protein A Dynabeads by blocking for 3h at room temperature in 1 mL blocking buffer, washing once with PBS-T and incubating for 1h at room temperature in 200 µL PBS-T with 5 µg anti-H3.3 (Active Motif, 91191), 10 µg anti-CENP-A (Cell Signaling, 2186), or 10 µg control IgG (Abcam, ab46540) antibodies. After a wash in binding buffer, we added the antibody-coupled beads to the chromatin and incubated overnight at 4°C on a rotating wheel. The next day, beads were recovered using a magnetic rack and sequentially washed with appropriate buffers. Beads were treated with RNase A and proteinase K in the presence of 2% SDS. DNA was purified using AMPure XP beads (Beckman Coulter, A63880) as per the manufacturer’s protocol and eluted in nuclease-free water.","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."],"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":["ChIP-seq"],"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":"CENP-A and H3.3 ChIP-seq of 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 its localization at EMT gene loci. 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. We performed bulk ChIP-seq experiments at the same time points as our transcriptomic data (day 10 and 24). In order to profile changes in CENP-A localization, 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":"2026-04-24T16:02:10.245Z","creation":"2025-09-08T12:13:52.873Z"},"accession":"E-MTAB-15579","cross_references":{"ENA":["ERP179765"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002692","EFO_0005518","EFO_0004184"]}}