ArticleGenome biology2024
scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- DUET-seq: An Open-Source Droplet Platform for High-Fidelity Joint Chromatin and Transcriptome Profiling Reveals Temporal Regulatory Decoupling in Single Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Multimodal single cell analysis reveals a link between flowering and leaf initiation.bioRxiv : the preprint server for biology · 2026Article
- Empirical Estimation of Ambient Contamination in Combinatorial Single-Cell Methods Using Multi-Reference Mapping.bioRxiv : the preprint server for biology · 2026Article
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
- Methodologies for Sample Multiplexing and Computational Deconvolution in Single-Cell Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Review
- WUSCHEL-dependent chromatin regulation in maize inflorescence development at single-cell resolution.Genome biology · 2025Article
- A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution.Nature plants · 2025Article
- Exploring the untapped potential of single-cell and spatial omics in plant biology.The New phytologist · 2025Review
- Through the lens of bioenergy crops: advances, bottlenecks, and promises of plant engineering.The Plant journal : for cell and molecular biology · 2025Review
- The Application of Single-Cell Technologies for Vaccine Development Against Viral Infections.Vaccines · 2025Review
- Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics.Nature methods · 2025Article
- Scalable eQTL mapping using single-nucleus RNA-sequencing of recombined gametes from a small number of individuals.PLoS biology · 2025Article
- Plant engineering: advances, bottlenecks, and promise.The Plant journal : for cell and molecular biology · 2025Article
- Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC.bioRxiv : the preprint server for biology · 2025Article
- Article
- From chromatin to crop: epigenetic innovations in bioenergy systems.Frontiers in plant science · 2025Review
- A spatially resolved multiomic single-cell atlas of soybean development.bioRxiv : the preprint server for biology · 2024Article
- scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing.Genome biology · 2024Article
- Mind the gap: Epigenetic regulation of chromatin accessibility in plants.Plant physiology · 2024Review
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Authors and funding
4 authors.
Funding
Abstract
Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput and high costs. Here, we present a novel technique called scifi-ATAC-seq, single-cell combinatorial fluidic indexing ATAC-sequencing, which combines a barcoded Tn5 pre-indexing step with droplet-based single-cell ATAC-seq using the 10X Genomics platform. With scifi-ATAC-seq, up to 200,000 nuclei across multiple samples can be indexed in a single emulsion reaction, representing an approximately 20-fold increase in throughput compared to the standard 10X Genomics workflow.
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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.