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| Status |
Public on Oct 21, 2021 |
| Title |
Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC [Species_Mix_GFP] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
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.
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| Overall design |
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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| Contributor(s) |
Fiškin E, Lareau C |
| Citation(s) |
34675424 |
| |
| Submission date |
Sep 04, 2020 |
| Last update date |
Jan 20, 2022 |
| Contact name |
Caleb Lareau |
| E-mail(s) |
[email protected]
|
| Organization name |
Memorial Sloan Kettering
|
| Street address |
417 E 68th St, Zuckerman - ZRC 1132
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE157486 |
Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC |
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| Relations |
| BioProject |
PRJNA661464 |
| SRA |
SRP280099 |
