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Txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility.

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.

SUBMITTER: Zhang H 

PROVIDER: S-EPMC10958877 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility.

Zhang Hao H   Mulqueen Ryan M RM   Iannuzo Natalie N   Farrera Dominique O DO   Polverino Francesca F   Galligan James J JJ   Ledford Julie G JG   Adey Andrew C AC   Cusanovich Darren A DA  

Genome biology 20240322 1

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 underappreciate  ...[more]

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