{"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-16636"],"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 41 days post-induction to profile changes in CENP-A localization in cells expressing either basal CENP-A levels (non-induced, control with no Dox cultivated for 41 days), high CENP-A levels (induced for 41 days with 10 ng/ml Dox) or reversed from high to basal CENP-A levels (induction for 24 days followed by interruption for 17 days)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - MCF-10-2A TetOn-CENPA-FLAG-HA cells stably expressing a dominant-negative p53 vector (p53-DN) were cultured for 41 days in the absence (no Dox), presence of Dox (10 ng/mL) or with interrupted induction with Dox (10ng/mL Dox for 24 days followed by 17 days without Dox) to induce basal or high CENP-A expression. Culture medium (+/- Dox) was renewed every 2-3 days. We harvested cells at day 41 post-induction.","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.","Nucleic Acid Extraction - For each IP, 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.","Sequencing - Sequencing was perfomred on the Illumina NextSeq 2000 at the Institut Curie Next Generation Sequencing (NGS) platform."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"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 ChIP-seq of MCF10-2A cells to study CENP-A localization following reversal from high to basal CENP-A expression","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 41 days post-induction to profile changes in CENP-A localization in cells expressing either basal CENP-A levels (non-induced, control with no Dox cultivated for 41 days), high CENP-A levels (induced for 41 days with 10 ng/ml Dox) or reversed from high to basal CENP-A levels (induction for 24 days followed by interruption for 17 days).","dates":{"release":"2026-04-24T00:00:00Z","modification":"2026-04-24T16:03:38.921Z","creation":"2026-02-11T11:22:32.791Z"},"accession":"E-MTAB-16636","cross_references":{"ENA":["ERP188991"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002692","EFO_0005518","EFO_0004184"]}}