txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility
Posted on 2024-08-15 - 03:16
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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Zhang, Hao; Mulqueen, Ryan M.; Iannuzo, Natalie; Farrera, Dominique O.; Polverino, Francesca; Galligan, James J.; et al. (2024). txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.7146511.v1