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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URL: https://www.ncbi.nlm.nih.gov/pubmed/29190363
DOI: 10.1093/nar/gkx1206

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 > cell lineage tracing
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

Investigative techniques and equipment > assays > next generation sequencing
CSHL Authors:
Communities: CSHL labs > Lee lab
CSHL labs > Zador lab
CSHL Cancer Center Program > Cancer Genetics
Depositing User: Matt Covey
Date: 28 February 2018
Date Deposited: 08 Dec 2017 17:19
Last Modified: 12 Jun 2018 16:02
PMCID: PMC5829746
Related URLs:
URI: http://repository.cshl.edu/id/eprint/35709

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