Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC [Species_Mix_GFP]
UID: 10870
- Description
- Summary from GEO:
"Single cell multi-omic readouts of both the cellular transcriptome and proteome have significantly enhanced our ability to comprehensively characterize cellular states. Most approaches in this area rely on oligonucleotide barcode-conjugated antibodies that target cell surface epitopes of interest, enabling their concomitant detection with the transcriptome. However, a similar high-throughput measurement of other cellular modalities such as the epigenome in concert with protein levels have not been described. Moreover, detection of epitopes is limited to antigens for which a specific antibody is available. Here, we introduce PHAGE-ATAC, an approach that enables the scalable and simultaneous detection of protein levels and chromatin accessibility data in single cells using the assay of transposase-accessible chromatin with sequencing (ATAC-seq). Quantitative detection of proteins by PHAGE-ATAC is accomplished through the use of engineerable nanobody-displaying phages that are genetically barcoded within the nanobody-encoding phagemids. We demonstrate the utility of PHAGE-ATAC for multimodal single cell genomic analysis in both cell lines and primary human cells. Analogous to phage display approaches, we further establish a synthetic high-complexity library of nanobody-displaying phages and demonstrate its utility to select novel antigen-specific nanobodies for PHAGE-ATAC."
Overall design from GEO:
"A 2:1:1 ratio of NIH3T3, EGFP+ HEK293T, and EGFP- HEK29T3 were stained with phages against EGFP carrying a known anti-EGFP nanobody. Cell mixtures were then processed using a modified scATAC-seq protocol."
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Access via GEO
Accession #: GSE157485Access via BioProject
Accession #: PRJNA661464Access via SRA
Accession #: SRP280099 - Access Restrictions
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Free to All
- Access Instructions
- The NCBI Gene Expression Omnibus, SRA and BioProject databases provide open access to these files.
- Associated Publications
- Equipment Used
- Dataset Format(s)
- CSV, TSV, TAR
- Dataset Size
- 1 GB
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