{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Zhang H"],"funding":["National Institute of Environmental Health Sciences","NIEHS NIH HHS","NIMH NIH HHS","NHLBI NIH HHS","National Heart, Lung, and Blood Institute","National Institute of Mental Health","National Institute of General Medical Sciences","NIGMS NIH HHS"],"pagination":["78"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10958877"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["25(1)"],"pubmed_abstract":["We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16<sup>-/-</sup>) model. Our study of CC16<sup>-/-</sup> nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model."],"journal":["Genome biology"],"pubmed_title":["txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility."],"pmcid":["PMC10958877"],"funding_grant_id":["R35 GM137896","RF1 MH128842","R35 GM137910","T32 ES007091","T32ES007091","R35GM124704","RF1MH128842","R35 GM124704","R01 HL142769","R35GM137910","R01HL142769","R35GM137896","P30 ES006694"],"pubmed_authors":["Cusanovich DA","Galligan JJ","Iannuzo N","Zhang H","Mulqueen RM","Polverino F","Farrera DO","Ledford JG","Adey AC"],"additional_accession":[]},"is_claimable":false,"name":"txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility.","description":"We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16<sup>-/-</sup>) model. Our study of CC16<sup>-/-</sup> nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Mar","modification":"2026-06-02T10:38:00.702Z","creation":"2025-04-06T00:49:25.834Z"},"accession":"S-EPMC10958877","cross_references":{"pubmed":["38519979"],"doi":["10.1186/s13059-023-03150-1"]}}