ZipSeq: Barcoding for Real-time Mapping of Single Cell Transcriptomes

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2020 Jul 8

PMID 32632238

Citations 66

Authors

Kenneth H Hu

John P Eichorst

Chris S McGinnis

David M Patterson

Eric D Chow

Kelly Kersten

Stephen C Jameson

Zev J Gartner

Arjun A Rao

Matthew F Krummel

Affiliations

Soon will be listed here.

Abstract

Spatial transcriptomics seeks to integrate single cell transcriptomic data within the three-dimensional space of multicellular biology. Current methods to correlate a cell's position with its transcriptome in living tissues have various limitations. We developed an approach, called 'ZipSeq', that uses patterned illumination and photocaged oligonucleotides to serially print barcodes ('zipcodes') onto live cells in intact tissues, in real time and with an on-the-fly selection of patterns. Using ZipSeq, we mapped gene expression in three settings: in vitro wound healing, live lymph node sections and a live tumor microenvironment. In all cases, we discovered new gene expression patterns associated with histological structures. In the tumor microenvironment, this demonstrated a trajectory of myeloid and T cell differentiation from the periphery inward. A combinatorial variation of ZipSeq efficiently scales in the number of regions defined, providing a pathway for complete mapping of live tissues, subsequent to real-time imaging or perturbation.

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