GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE157485 Query DataSets for GSE157485
Status Public on Oct 21, 2021
Title Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC [Species_Mix_GFP]
Organisms Homo sapiens; Mus musculus
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 A 2:1:1 ratio of NIH3T3, EGFP+ HEK293T, and EGFP- HEK29T3 were stained with phages against EGFP carrying a known anti-EGFP nanobody. Cell mixtures were then processed using a modified scATAC-seq protocol.
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)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
Samples (2)
GSM4766876 SpeciesMix_eGFP_Known_ATAC
GSM4766877 SpeciesMix_eGFP_Known_Phage
This SubSeries is part of SuperSeries:
GSE157486 Single cell analysis of protein epitopes and chromatin accessibility using PHAGE-ATAC
BioProject PRJNA661464
SRA SRP280099

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE157485_RAW.tar 1.0 Gb (http)(custom) TAR (of CSV, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap