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Single-cell multi-modal profiling of proteins and chromatin accessibility using PHAGE-ATAC [Intracellular_GFP]

UID: 10872

Author(s): Fiskin, Evgenji, Lareau, Caleb A.* * MSK affiliated

Description
Summary from GEO:

"Multi-modal measurements of single cell profiles are a powerful tool for characterizing cell states and regulatory mechanisms. While current methods allow profiling of RNA along with either readouts of chromatin or protein, connecting chromatin state to protein levels remains a barrier. Here, we developed PHAGE-ATAC, a method that uses engineered camelid single-domain antibody (‘nanobody’)-displaying phages for simultaneous single-cell measurement of surface proteins, chromatin accessibility profiles, and mtDNA-based clonal tracing through a single-cell and massively parallel droplet-based assay of transposase-accessible chromatin with sequencing (ATAC-seq). We demonstrate PHAGE-ATAC for multimodal analysis in primary human immune cells, for multiplexing, for intracellular protein analysis, and for the detection of SARS-CoV-2 spike protein. Finally, we construct a synthetic high-complexity phage library for selection of novel antigen-specific nanobodies that bind cells of particular molecular profiles, opening a new avenue for protein detection, cell characterization and screening with single-cell genomics."

Overall design from GEO:

"293T cells expressing cytosolic EGFP were fixed, lysed and then incubated with an anti-EGFP phage nanobody and processed for PHAGE-ATAC."
Subject of Study
Subject(s)
Access via GEO


Accession #: GSE172921

Access via BioProject


Accession #: PRJNA723636

Access via SRA


Accession #: SRP315792

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus, SRA and BioProject databases provide open access to these files.
Associated Publications
Equipment Used
Illumina NextSeq 550
Dataset Format(s)
CSV, TSV
Dataset Size
441.5 MB
Data Catalog Record Updated
2023-10-04