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txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility.
Zhang, Hao; Mulqueen, Ryan M; Iannuzo, Natalie; Farrera, Dominique O; Polverino, Francesca; Galligan, James J; Ledford, Julie G; Adey, Andrew C; Cusanovich, Darren A.
Affiliation
  • Zhang H; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA.
  • Mulqueen RM; Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA.
  • Iannuzo N; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA.
  • Farrera DO; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA.
  • Polverino F; Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, USA.
  • Galligan JJ; Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA.
  • Ledford JG; Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Arizona, Tucson, AZ, USA.
  • Adey AC; Banner - University Medicine North, Pulmonary - Clinic F, Tucson, AZ, USA.
  • Cusanovich DA; Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, USA.
Genome Biol ; 25(1): 78, 2024 03 22.
Article in En | MEDLINE | ID: mdl-38519979
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-/-) model. Our study of CC16-/- 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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Chromatin / Chromatin Immunoprecipitation Sequencing Limits: Animals / Humans Language: En Journal: Genome Biol Journal subject: BIOLOGIA MOLECULAR / GENETICA Year: 2024 Document type: Article Affiliation country: United States
Fulltext
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Chromatin / Chromatin Immunoprecipitation Sequencing Limits: Animals / Humans Language: En Journal: Genome Biol Journal subject: BIOLOGIA MOLECULAR / GENETICA Year: 2024 Document type: Article Affiliation country: United States