Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing
- Brendan L. O'Connell1,
- Ruth V. Nichols1,
- Dmitry Pokholok2,
- Jerushah Thomas2,
- Sonia N. Acharya1,
- Andrew Nishida1,
- Casey A. Thornton1,
- Marissa Co1,
- Andrew J. Fields1,
- Frank J. Steemers2 and
- Andrew C. Adey1,3,4,5
- 1Oregon Health & Science University, Department of Molecular and Medical Genetics, Portland, Oregon 97239, USA;
- 2ScaleBio, San Diego, California 92121, USA;
- 3Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon 97239, USA;
- 4Oregon Health & Science University, Cancer Early Detection Advanced Research Center, Portland, Oregon 97239, USA;
- 5Oregon Health & Science University, Knight Cardiovascular Institute, Portland, Oregon 97239, USA
Abstract
Here we present advancements in single-cell combinatorial indexed Assay for Transposase Accessible Chromatin (sciATAC) to measure chromatin accessibility that leverage nanowell chips to achieve atlas-scale cell throughput (>105 cells) at low cost. The platform leverages the core of the sciATAC workflow where multiple indexed tagmentation reactions are performed, followed by pooling and distribution to a second set of reaction wells for polymerase chain reaction (PCR)-based indexing. In this work, we instead leverage a chip containing 5184 nanowells at the PCR stage of indexing, enabling a 52-fold improvement in scale and reduction in per-cell preparation costs. We detail three variants that balance cell throughput and depth of coverage, and apply these methods to banked mouse brain tissue, producing maps of cell types as well as neuronal subtypes that include integration with existing single-cell Assay for Transposase Accessible Chromatin (scATAC) and scRNA-seq data sets. Our optimized workflow achieves a high fraction of reads that fall within called peaks (>80%) and low cell doublet rates. The high cell coverage technique produces high unique reads per cell, while retaining high enrichment for open chromatin regions, enabling the assessment of >70,000 unique accessible loci on average for each cell profiled. When compared to current methods in the field, our technique provides similar or superior per-cell information with very low levels of cell-to-cell cross talk, and achieves this at a cost point much lower than existing assays.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.276655.122.
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Freely available online through the Genome Research Open Access option.
- Received January 31, 2022.
- Accepted December 8, 2022.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
