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Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

Authors
Eleni P. Mimitou,Caleb A. Lareau
Kelvin Y. Chen,Andre L. Zorzetto-Fernandes,Yuhan Hao,Yusuke Takeshima,Wendy Luo,Tse-Shun Huang,Bertrand Z. Yeung,Efthymia Papalexi,Pratiksha I. Thakore,Tatsuya Kibayashi,James Badger Wing,Mayu Hata,Rahul Satija,Kristopher L. Nazor,Shimon Sakaguchi,Leif S. Ludwig,Vijay G. Sankaran,Aviv Regev,Peter Smibert,Eleni Mimitou,Leif Ludwig,Vijay Sankaran,Kristopher Nazor,Caleb Lareau,Kelvin Chen,Andre Zorzetto-Fernandes,Tse Huang,Bertrand Yeung,Pratiksha Thakore
+29 authors
,James Wing
Published
Jun 3, 2021
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Abstract

Recent technological advances have enabled massively parallel chromatin profiling with scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here we present ATAC with select antigen profiling by sequencing (ASAP-seq), a tool to simultaneously profile accessible chromatin and protein levels. Our approach pairs sparse scATAC-seq data with robust detection of hundreds of cell surface and intracellular protein markers and optional capture of mitochondrial DNA for clonal tracking, capturing three distinct modalities in single cells. ASAP-seq uses a bridging approach that repurposes antibody:oligonucleotide conjugates designed for existing technologies that pair protein measurements with single-cell RNA sequencing. Together with DOGMA-seq, an adaptation of CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) for measuring gene activity across the central dogma of gene regulation, we demonstrate the utility of systematic multi-omic profiling by revealing coordinated and distinct changes in chromatin, RNA and surface proteins during native hematopoietic differentiation and peripheral blood mononuclear cell stimulation and as a combinatorial decoder and reporter of multiplexed perturbations in primary T cells. Chromatin accessibility, gene expression and protein levels are measured in the same single cell.

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