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Series GSE172921 Query DataSets for GSE172921
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
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 293T cells expressing cytosolic EGFP were fixed, lysed and then incubated with an anti-EGFP phage nanobody 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
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)
GSM5259071 Intracellular_GFP_ATAC
GSM5259072 Intracellular_GFP_Phage
This SubSeries is part of SuperSeries:
GSE157486 Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC
BioProject PRJNA723636
SRA SRP315792

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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
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Raw data are available in SRA
Processed data are available on Series record

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