ArticleNature biotechnology2021
High-content single-cell combinatorial indexing.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 108 citations in OpenAlex.
- Sequential-GAM constructs the single-cell geometric 3D genome structure.Nucleic acids research · 2026Article
- A medium throughput approach for single cell copy number variation sequencing towards efficient application in clinics.Journal of advanced research · 2026Article
- The cardiac 4D nucleome: nuclear and chromatin dynamics across development, disease and ageing.Nature reviews. Cardiology · 2026Review
- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- Exploring single-cell and multi-omics technologies and their role in unraveling tumor heterogeneity of hepatocellular carcinoma.Journal of liver cancer · 2026Review
- PU.1 inhibition sensitizes stem-monocytic AML to BCL2 blockade.bioRxiv : the preprint server for biology · 2026Article
- Methodologies for Sample Multiplexing and Computational Deconvolution in Single-Cell Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Unraveling the interplay of DNA methylation and chromosome organization.Biochemical Society transactions · 2025Review
- SCRIPT: Predicting Single-Cell Long-Range Cis-Regulation Based on Pretrained Graph Attention Networks.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Chromosome-level genome assembly of Turpan wonder gecko (Teratoscincus roborowskii) reveals olfactory candidate genes.Scientific data · 2025Article
- Whole-genome methylation profiling of extracellular vesicle DNA in gastric cancer identifies intercellular communication features.Nature communications · 2025Article
- Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq.Science advances · 2025Article
- IT-scC&T-seq streamlines scalable, parallel profiling of protein-DNA interactions in single cells.Genome biology · 2025Article
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics.Nature methods · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- Semi-automated IT-scATAC-seq profiles cell-specific chromatin accessibility in differentiation and peripheral blood populations.Nature communications · 2025Article
- Single-Cell Hi-C Technologies and Computational Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.Nucleic acids research · 2025Article
- Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics.Cell discovery · 2025Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Single-cell combinatorial indexing (sci) with transposase-based library construction increases the throughput of single-cell genomics assays but produces sparse coverage in terms of usable reads per cell. We develop symmetrical strand sci ('s3'), a uracil-based adapter switching approach that improves the rate of conversion of source DNA into viable sequencing library fragments following tagmentation. We apply this chemistry to assay chromatin accessibility (s3-assay for transposase-accessible chromatin, s3-ATAC) in human cortical and mouse whole-brain tissues, with mouse datasets demonstrating a six- to 13-fold improvement in usable reads per cell compared with other available methods. Application of s3 to single-cell whole-genome sequencing (s3-WGS) and to whole-genome plus chromatin conformation (s3-GCC) yields 148- and 14.8-fold improvements, respectively, in usable reads per cell compared with sci-DNA-sequencing and sci-HiC. We show that s3-WGS and s3-GCC resolve subclonal genomic alterations in patient-derived pancreatic cancer cell lines. We expect that the s3 platform will be compatible with other transposase-based techniques, including sci-MET or CUT&Tag.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.