ArticleeLife2022
Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 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
- Developing mouse inhibitory neuron single-cell transcriptomes reveal distinct modes of cell-type diversification.Nature neuroscience · 2026Article
- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- Human microglial transitions at the Aβ-tau inflection point associate with divergent pathways to dementia and resilience.Nature medicine · 2026Article
- Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling.Nature communications · 2026Article
- CapMux: a Snakemake pipeline for early demultiplexing of split-pool scRNA-seq data into sample-resolved outputs.Frontiers in bioinformatics · 2026Article
- Decoding cnidarian cell type gene regulation.Nature ecology & evolution · 2026Article
- USPPAR is a cost-effective, scalable, and highly sensitive single-cell RNA sequencing workflow compatible with diverse specimens.PLoS biology · 2025Article
- Single-Cell Transcriptomics in Inherited Retinal Dystrophies: Current Findings and Emerging Perspectives.Genes · 2025Review
- Integrated ambient modeling and genetic demultiplexing of single-cell RNA+ATAC multiome experiments with Ambimux.bioRxiv : the preprint server for biology · 2025Article
- Chromatin accessibility provides a window into the genetic etiology of human brain disease.Trends in genetics : TIG · 2025Review
- Barcodes based on nucleic acid sequences: Applications and challenges (Review).Molecular medicine reports · 2025Review
- Semi-automated IT-scATAC-seq profiles cell-specific chromatin accessibility in differentiation and peripheral blood populations.Nature communications · 2025Article
- From specialization to broad adoption: Key trends in droplet microfluidic innovations enhancing accessibility to non-experts.Biomicrofluidics · 2025Article
- A single-cell transcriptomic atlas of developing inhibitory neurons reveals expanding and contracting modes of diversification.bioRxiv : the preprint server for biology · 2025Article
- inDrops-2: a flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples.Nucleic acids research · 2025Article
- scTrends: A living review of commercial single-cell and spatial 'omic technologies.Cell genomics · 2024Review
- scBlood: A comprehensive single-cell accessible chromatin database of blood cells.Computational and structural biotechnology journal · 2024Article
- Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling.Nature communications · 2024Article
- Spectral neural approximations for models of transcriptional dynamics.Biophysical journal · 2024Article
Corrections and comments
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Authors and funding
13 authors.
Funding
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Abstract
Single-cell RNA-seq and single-cell assay for transposase-accessible chromatin (ATAC-seq) technologies are used extensively to create cell type atlases for a wide range of organisms, tissues, and disease processes. To increase the scale of these atlases, lower the cost and pave the way for more specialized multiome assays, custom droplet microfluidics may provide solutions complementary to commercial setups. We developed HyDrop, a flexible and open-source droplet microfluidic platform encompassing three protocols. The first protocol involves creating dissolvable hydrogel beads with custom oligos that can be released in the droplets. In the second protocol, we demonstrate the use of these beads for HyDrop-ATAC, a low-cost noncommercial scATAC-seq protocol in droplets. After validating HyDrop-ATAC, we applied it to flash-frozen mouse cortex and generated 7996 high-quality single-cell chromatin accessibility profiles in a single run. In the third protocol, we adapt both the reaction chemistry and the capture sequence of the barcoded hydrogel bead to capture mRNA, and demonstrate a significant improvement in throughput and sensitivity compared to previous open-source droplet-based scRNA-seq assays (Drop-seq and inDrop). Similarly, we applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes closely matching reference single-cell gene expression data. Finally, we leveraged HyDrop-RNA's high capture rate to analyze a small population of fluorescence-activated cell sorted neurons from the
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