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Series GSE157483 Query DataSets for GSE157483
Status Public on Oct 21, 2021
Title Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC [Human_PBMCs]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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.
Overall design Human PBMCs were stained with Phages displaying anti-CD4, CD8, or CD16 nanobodies to quantify protein abundances along side accessible chromatin using scATAC-seq
Contributor(s) Fiškin E, Lareau C
Citation(s) 34675424
Submission date Sep 04, 2020
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)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (4)
GSM4766872 PBMC_Channel1_ATAC
GSM4766873 PBMC_Channel1_Phage
GSM4766874 PBMC_Channel2_ATAC
This SubSeries is part of SuperSeries:
GSE157486 Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC
BioProject PRJNA661463
SRA SRP280097

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Supplementary file Size Download File type/resource
GSE157483_RAW.tar 1.6 Gb (http)(custom) TAR (of CSV, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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