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

UID: 11056

Author(s): Mimitou, Eleni P.*, Lareau, Caleb A.*, Chen, Kelvin Y., Ludwig, Leif S., Smibert, Peter* * MSK affiliated

Description
Summary from GEO:

"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."

Overall design from GEO:

"Mixed human and mouse cells were used to test the method's ability to detect antibody tags with specificity. A 50:50 cell mix was stained with a cocktail of human and mouse a-CD29 before fixation and lysis. Permeabilized cells were processed according to 10x scATAC workflow with the addition of a bridge oligo during the barcoding reaction in droplets to allow capture and barcoding of antibody tags."
Subject of Study
Homo sapiens
Mus musculus
Subject(s)
Cell Differentiation
Gene Expression Profiling
Hematopoiesis
Integrin beta1
Access via GEO


Accession #: GSE156475

Access via BioProject


Accession #: PRJNA658084

Access via SRA


Accession #: SRP278086

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus, BioProject, and SRA databases provides open access to these files
Associated Publications
Mimitou EP, Lareau CA, Chen KY, Zorzetto-Fernandes AL, Hao Y, Takeshima Y, Luo W, Huang TS, Yeung BZ, Papalexi E, Thakore PI, Kibayashi T, Wing JB, Hata M, Satija R, Nazor KL, Sakaguchi S, Ludwig LS, Sankaran VG, Regev A, Smibert P. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat Biotechnol. 2021 Oct;39(10):1246-1258. Epub 2021 Jun 3. PMID: 34083792; PMCID: PMC8763625.
Equipment Used
Illumina NextSeq 550

Sequencing and array capabilities for transcriptome, targeted resequencing and genotype sequencing

Dataset Format(s)
TSV, TAR
Dataset Size
846.6 MB
Data Catalog Record Updated
2023-11-22