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Series GSE172923 Query DataSets for GSE172923
Status Public on Oct 21, 2021
Title Single-cell multi-modal profiling of proteins and chromatin accessibility using PHAGE-ATAC [ASAP_Phage_comparison]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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 PBMCs were incubated with a panel of phage nanobodies or commercial TotalSeq-A antibodies and processed for PHAGE-ATAC, PHAGE-ASAP or ASAP-seq
Contributor(s) Fiškin E, Lareau C
Citation(s) 34675424
Submission date Apr 21, 2021
Last update date Jan 20, 2022
Contact name Caleb Lareau
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 (7)
GSM5259074 PBMC_ASAP_Phage_compare_A_ADT
GSM5259075 PBMC_ASAP_Phage_compare_A_ATAC
GSM5259076 PBMC_ASAP_Phage_compare_B_ADT
This SubSeries is part of SuperSeries:
GSE157486 Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC
BioProject PRJNA723635
SRA SRP315791

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Supplementary file Size Download File type/resource
GSE172923_ASAP_phage_comparison_singlecell_counts.csv.gz 6.9 Mb (ftp)(http) CSV
GSE172923_asap_phage_comparison_fragments.tsv.gz 1.6 Gb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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