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Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

View ORCID ProfileXiaoyin Chen, Yu-Chi Sun, George M Church, Je Hyuk Lee, View ORCID ProfileAnthony M Zador
doi: https://doi.org/10.1101/180323
Xiaoyin Chen
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Yu-Chi Sun
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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George M Church
2Wyss Institute, Harvard Medical School, Boston, Massachusetts, USA
3Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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Je Hyuk Lee
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Anthony M Zador
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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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 tradeoff 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.

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Posted August 24, 2017.
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Efficient in situ barcode sequencing using padlock probe-based BaristaSeq
Xiaoyin Chen, Yu-Chi Sun, George M Church, Je Hyuk Lee, Anthony M Zador
bioRxiv 180323; doi: https://doi.org/10.1101/180323
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Efficient in situ barcode sequencing using padlock probe-based BaristaSeq
Xiaoyin Chen, Yu-Chi Sun, George M Church, Je Hyuk Lee, Anthony M Zador
bioRxiv 180323; doi: https://doi.org/10.1101/180323

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