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Series GSE172920 Query DataSets for GSE172920
Status Public on Oct 21, 2021
Title Single-cell multi-modal profiling of proteins and chromatin accessibility using PHAGE-ATAC [Spike_mix_pbmcs]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
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.
 
Overall design A mix of PBMCs and 293T cells expressing either membrane-exposed EGFP-GPI or the SARS-CoV-2 spike protein were incubated with a panel of phage nanobodies and processed for PHAGE-ATAC
 
Contributor(s) Fiškin E, Lareau C
Citation(s) 34675424
Submission date Apr 21, 2021
Last update date Jan 20, 2022
Contact name Caleb Lareau
E-mail(s) lareauc@mskcc.org
Organization name Memorial Sloan Kettering
Street address 417 E 68th St, Zuckerman - ZRC 1132
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (2)
GSM5259069 PBMC_293T_Mix_ATAC
GSM5259070 PBMC_293T_Mix_Phage
This SubSeries is part of SuperSeries:
GSE157486 Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC
Relations
BioProject PRJNA723634
SRA SRP315790

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Supplementary file Size Download File type/resource
GSE172920_SpikeMix_singlecell_counts.csv.gz 6.8 Mb (ftp)(http) CSV
GSE172920_spike_mix_fragments.tsv.gz 767.3 Mb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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