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High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [mouse brain]

ABSTRACT: High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [mouse brain]

PROVIDER: PRJNA509254 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8310670_1.fastq.gz	Fastqsanger.gz
	SRR8310670_2.fastq.gz	Fastqsanger.gz
	SRR8310680_1.fastq.gz	Fastqsanger.gz
	SRR8310680_2.fastq.gz	Fastqsanger.gz
	SRR8310690_1.fastq.gz	Fastqsanger.gz

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Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing [RNA-seq]

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Project description:Cell atlas projects and high-throughput perturbation screens require single-cell sequencing at a scale that is challenging with current technology. To enable cost-effective single-cell sequencing for millions of individual cells, we developed “single-cell combinatorial fluidic indexing” (scifi). The scifi-RNA-seq assay combines one-step combinatorial pre-indexing of entire transcriptomes inside permeabilized cells with subsequent single-cell RNA-seq using microfluidics. Pre-indexing allows us to load multiple cells per droplet and bioinformatically demultiplex their individual expression profiles. Thereby, scifi-RNA-seq massively increases the throughput of droplet-based single-cell RNA-seq, and it provides a straightforward way of multiplexing thousands of samples in a single experiment. Compared to multi-round combinatorial indexing, scifi-RNA-seq provides an easier, faster, and more efficient workflow. In contrast to cell hashing methods, which flag and discard droplets containing more than one cell, scifi-RNA-seq resolves and retains individual transcriptomes from overloaded droplets.

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