Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

Chen, X., Sun, Y. C., Church, G. M., Lee, J. H., Zador, A. M. (February 2018) Efficient in situ barcode sequencing using padlock probe-based BaristaSeq. Nucleic Acids Res, 46 (4). e22. ISSN 0305-1048

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Abstract

Cellular DNA/RNA tags (barcodes) allow for multiplexed cell lineage tracing and neuronal projection mapping with cellular resolution. Conventional approaches to reading out cellular barcodes trade off spatial resolution with throughput. Bulk sequencing achieves high throughput but sacrifices spatial resolution, whereas manual cell picking has low throughput. In situ sequencing could potentially achieve both high spatial resolution and high throughput, but current in situ sequencing techniques are inefficient at reading out cellular barcodes. Here we describe BaristaSeq, an optimization of a targeted, padlock probe-based technique for in situ barcode sequencing compatible with Illumina sequencing chemistry. BaristaSeq results in a five-fold increase in amplification efficiency, with a sequencing accuracy of at least 97%. BaristaSeq could be used for barcode-assisted lineage tracing, and to map long-range neuronal projections.

Item Type:	Paper
Subjects:	Investigative techniques and equipment Investigative techniques and equipment > assays Investigative techniques and equipment > cell lineage tracing organs, tissues, organelles, cell types and functions > cell types and functions > cell types organs, tissues, organelles, cell types and functions > cell types and functions > cell types organs, tissues, organelles, cell types and functions > cell types and functions > cell types organs, tissues, organelles, cell types and functions > cell types and functions organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal projections organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal projections organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal projections organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons Investigative techniques and equipment > assays > next generation sequencing organs, tissues, organelles, cell types and functions
CSHL Authors:	Lee, Je Hyuk Zador, Anthony M. Sun, Yu-Chi Chen, Xiaoyin
Communities:	CSHL Cancer Center Program > Cancer Genetics CSHL labs > Lee lab CSHL labs > Zador lab CSHL Cancer Center Program > Cancer Genetics and Genomics Program
Depositing User:	Matt Covey
Date:	28 February 2018
Date Deposited:	08 Dec 2017 17:19
Last Modified:	07 Feb 2024 18:47
PMCID:	PMC5829746
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/35709

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