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| Status |
Public on Oct 21, 2021 |
| Title |
Single-cell multi-modal profiling of proteins and chromatin accessibility using PHAGE-ATAC [Intracellular_GFP] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
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.
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| Overall design |
293T cells expressing cytosolic EGFP were fixed, lysed and then incubated with an anti-EGFP phage nanobody and processed for PHAGE-ATAC
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| Contributor(s) |
Fiškin E, Lareau C |
| Citation(s) |
34675424 |
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| Submission date |
Apr 21, 2021 |
| Last update date |
Jan 20, 2022 |
| Contact name |
Caleb Lareau |
| E-mail(s) |
lareauc@mskcc.org
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| Organization name |
Memorial Sloan Kettering
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| 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) |
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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 |
PRJNA723636 |
| SRA |
SRP315792 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE172921_Intracellular_singlecell_counts.csv.gz |
3.4 Mb |
(ftp)(http) |
CSV |
| GSE172921_egfp_intracellular_fragments.tsv.gz |
438.1 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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