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Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets

ABSTRACT: Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets

OTHER RELATED OMICS DATASETS IN: GSE70151GSE63269EGAD00001006080EGAS00001004381

PROVIDER: PRJNA267855 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1748411_1.fastq.gz	Fastqsanger.gz
	SRR1748411_2.fastq.gz	Fastqsanger.gz
	SRR1748412_1.fastq.gz	Fastqsanger.gz
	SRR1748412_2.fastq.gz	Fastqsanger.gz
	SRR1853180_1.fastq.gz	Fastqsanger.gz

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Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets

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Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets

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Project description:Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. VIDEO ABSTRACT.

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Sequencing data for single cells and DNA-functionalized microbeads encapsulated in hydrogel droplets.

Project description:DNA barcodes can be used to identify single cells in a sequencing data space while optical codes can be used to track single live cells in an image data space. We have developed dual image and DNA (ID)-coding, which identifies individual single cells in both live image and sequencing data spaces. Samples provided here are relevant to proof-of-concept studies of ID-coding presented in the associated publication. DNA barcoded micro-particles were encapsulated in hydrogel droplets with or without single cells. The hydrogel droplets were then subjected to “single-droplet sequencing” where whole polyA-bearing nucleic acid components within a hydrogel droplet (i.e. mRNA from cells and synthetic DNA on beads) were concatenated by the same cell barcodes.

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