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Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC [CD8_Hashing]

UID: 10868

Author(s): Fiskin, Evgenji, Lareau, Caleb A.* * MSK affiliated

Description
Summary from GEO:

"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 from GEO:
"Four donors' CD8 T-cells were hashed using uniquely barcoded anti-CD8 phages, pooled, and then processed using a modified scATAC-seq protocol. Hashing concordance with donor genotype was measured and assessed (see CD8_Human_T-cell_Hashing_barcode-assignments.csv.gz)."
Subject of Study
Homo sapiens
Subject(s)
Chromatin Immunoprecipitation Sequencing
Single-Cell Analysis
Transcriptome
Access via GEO


Accession #: GSE157478

Access via BioProject


Accession #: PRJNA661454

Access via SRA


Accession #: SRP280094

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus, SRA and BioProject databases provide open access to these files.
Associated Publications
Fiskin E, Lareau CA, Ludwig LS, Eraslan G, Liu F, Ring AM, Xavier RJ, Regev A. Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC. Nat Biotechnol. 2022 Mar;40(3):374-381. Epub 2021 Oct 21. PMID: 34675424.
Equipment Used
Illumina NextSeq 500
Dataset Format(s)
CSV, TAR
Dataset Size
553.615 MB
Data Catalog Record Updated
2023-10-04