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High throughput joint profiling of chromatin accessibility and protein levels in single cells [marrow]

ABSTRACT: High throughput joint profiling of chromatin accessibility and protein levels in single cells [marrow]

PROVIDER: PRJNA658082 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12476632_1.fastq.gz	Fastqsanger.gz
	SRR12476632_2.fastq.gz	Fastqsanger.gz
	SRR12476633_1.fastq.gz	Fastqsanger.gz
	SRR12476633_2.fastq.gz	Fastqsanger.gz
	SRR12476634_1.fastq.gz	Fastqsanger.gz

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Project description:Recent technological advances have enabled massively parallel single-cell Assay for Transposase Accessible Chromatin by sequencing (scATAC-seq) to simultaneously profile the epigenomic landscape in thousands of individual cells. scATAC-seq methods sample genomic DNA accessible to transposases, but have not previously been combined with measurement of protein levels. Here, we present ATAC with Select Antigen Profiling by sequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells, pairing sparse scATAC data with robust detection of hundreds of cell surface and intracellular protein markers, and optionally, enriched mtDNA coverage for lineage tracing (mtscATAC-seq) with minimal impact on ATAC-seq data quality. ASAP-seq makes use of a novel bridging approach to utilize existing commercially available antibody:oligo conjugates developed for CITE-seq and related technologies. We demonstrate the utility of ASAP-seq in the context of hematopoietic differentiation, cell surface marker dynamics following peripheral blood mononuclear cell stimulation, and as a combinatorial decoder of multiplexed perturbations in primary T cells.

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Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling

Project description:MultiPerturb-seq is a high-throughput CRISPR screening platform with joint single nucleus chromatin accessibility, transcriptome, and guide RNA capture. It uses combinatorial indexing combined with droplet microfluidics to scale throughput and integrate all three modalities. We apply MultiPerturb-seq to identify key genes whose loss can trigger differentiation in a rare pediatric cancer, atypical teratoid/rhabdoid tumor (AT/RT), which is driven by loss of the SWI/SNF chromatin remodeling subunit SMARCB1.

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Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels II

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