1. txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility
- Author
-
Hao Zhang, Ryan M. Mulqueen, Natalie Iannuzo, Dominique O. Farrera, Francesca Polverino, James J. Galligan, Julie G. Ledford, Andrew C. Adey, and Darren A. Cusanovich
- Subjects
Single-cell ,ATAC-seq ,Chromatin accessibility ,Combinatorial indexing ,Molecular hashing ,CC16 ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
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.
- Published
- 2024
- Full Text
- View/download PDF