ArticleNature communications2024
Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Single-cell insights into plant growth, adaptation, and evolution.Journal of integrative plant biology · 2026Review
- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- Genome-wide single-cell perturbation screens with VIPerturb-seq.bioRxiv : the preprint server for biology · 2026Article
- Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling.Nature communications · 2026Article
- Methodologies for Sample Multiplexing and Computational Deconvolution in Single-Cell Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states.Nature genetics · 2025Article
- Barcodes based on nucleic acid sequences: Applications and challenges (Review).Molecular medicine reports · 2025Review
- UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing.Nature methods · 2025Article
- Engineering next-generation microfluidic technologies for single-cell phenomics.Nature genetics · 2025Review
- Methods for multiplexing single-cell multi-omics.Nature methods · 2025Article
- From specialization to broad adoption: Key trends in droplet microfluidic innovations enhancing accessibility to non-experts.Biomicrofluidics · 2025Article
- Multiplets in scRNA-seq data: Extent of the problem and efficacy of methods for removal.PloS one · 2025Article
- Concepts and new developments in droplet-based single cell multi-omics.Trends in biotechnology · 2024Review
- Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling.Nature communications · 2024Article
Corrections and comments
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Authors and funding
20 authors.
Funding
Abstract
Multiomic profiling of single cells by sequencing is a powerful technique for investigating cellular diversity. Existing droplet-based microfluidic methods produce many cell-free droplets, underutilizing bead barcodes and reagents. Combinatorial indexing on microplates is more efficient for barcoding but labor-intensive. Here we present Overloading And unpacKing (OAK), which uses a droplet-based barcoding system for initial compartmentalization followed by a second aliquoting round to achieve combinatorial indexing. We demonstrate OAK's versatility with single-cell RNA sequencing as well as paired single-nucleus RNA sequencing and accessible chromatin profiling. We further showcase OAK's performance on complex samples, including differentiated bronchial epithelial cells and primary retinal tissue. Finally, we examine transcriptomic responses of over 400,000 melanoma cells to a RAF inhibitor, belvarafenib, discovering a rare resistant cell population (0.12%). OAK's ultra-high throughput, broad compatibility, high sensitivity, and simplified procedures make it a powerful tool for large-scale molecular analysis, even for rare cells.
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