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High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [human K562 and muring 3T3]

ABSTRACT: High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [human K562 and muring 3T3]

PROVIDER: PRJNA540583 | ENA |

REPOSITORIES: ENA

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

Project description:Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated prior to biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from over 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas. 3 replicates from GM12878 and HL-60 cell lines collected for differential gene expression analysis.

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High-content single-cell combinatorial indexing

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Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

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