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Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing

We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking of DNA barcodes onto complementary DNAs in situ...

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Autores principales: Kishi, Jocelyn Y., Liu, Ninning, West, Emma R., Sheng, Kuanwei, Jordanides, Jack J., Serrata, Matthew, Cepko, Constance L., Saka, Sinem K., Yin, Peng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9636025/
https://www.ncbi.nlm.nih.gov/pubmed/36216958
http://dx.doi.org/10.1038/s41592-022-01604-1
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author Kishi, Jocelyn Y.
Liu, Ninning
West, Emma R.
Sheng, Kuanwei
Jordanides, Jack J.
Serrata, Matthew
Cepko, Constance L.
Saka, Sinem K.
Yin, Peng
author_facet Kishi, Jocelyn Y.
Liu, Ninning
West, Emma R.
Sheng, Kuanwei
Jordanides, Jack J.
Serrata, Matthew
Cepko, Constance L.
Saka, Sinem K.
Yin, Peng
author_sort Kishi, Jocelyn Y.
collection PubMed
description We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking of DNA barcodes onto complementary DNAs in situ with a one-step DNA stitching reaction to create pooled, spatially indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full-transcriptome sequencing based on location, morphology or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three cellular layers and discovered biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only four to eight individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing.
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spelling pubmed-96360252022-11-06 Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing Kishi, Jocelyn Y. Liu, Ninning West, Emma R. Sheng, Kuanwei Jordanides, Jack J. Serrata, Matthew Cepko, Constance L. Saka, Sinem K. Yin, Peng Nat Methods Article We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking of DNA barcodes onto complementary DNAs in situ with a one-step DNA stitching reaction to create pooled, spatially indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full-transcriptome sequencing based on location, morphology or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three cellular layers and discovered biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only four to eight individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing. Nature Publishing Group US 2022-10-10 2022 /pmc/articles/PMC9636025/ /pubmed/36216958 http://dx.doi.org/10.1038/s41592-022-01604-1 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Kishi, Jocelyn Y.
Liu, Ninning
West, Emma R.
Sheng, Kuanwei
Jordanides, Jack J.
Serrata, Matthew
Cepko, Constance L.
Saka, Sinem K.
Yin, Peng
Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing
title Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing
title_full Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing
title_fullStr Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing
title_full_unstemmed Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing
title_short Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing
title_sort light-seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9636025/
https://www.ncbi.nlm.nih.gov/pubmed/36216958
http://dx.doi.org/10.1038/s41592-022-01604-1
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