CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics

High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that...

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Autores principales: Guo, Chuner, Kong, Wenjun, Kamimoto, Kenji, Rivera-Gonzalez, Guillermo C., Yang, Xue, Kirita, Yuhei, Morris, Samantha A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509836/
https://www.ncbi.nlm.nih.gov/pubmed/31072405
http://dx.doi.org/10.1186/s13059-019-1699-y
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author Guo, Chuner
Kong, Wenjun
Kamimoto, Kenji
Rivera-Gonzalez, Guillermo C.
Yang, Xue
Kirita, Yuhei
Morris, Samantha A.
author_facet Guo, Chuner
Kong, Wenjun
Kamimoto, Kenji
Rivera-Gonzalez, Guillermo C.
Yang, Xue
Kirita, Yuhei
Morris, Samantha A.
author_sort Guo, Chuner
collection PubMed
description High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are heritable, enabling cell populations to be tagged, pooled, and tracked over time in the same experimental replicate. We demonstrate the utility of CellTag Indexing by sequencing transcriptomes using a variety of cell types, including long-term tracking of cell engraftment and differentiation in vivo. Together, this presents CellTag Indexing as a broadly applicable genetic multiplexing tool that is complementary with existing single-cell technologies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1699-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-65098362019-06-05 CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics Guo, Chuner Kong, Wenjun Kamimoto, Kenji Rivera-Gonzalez, Guillermo C. Yang, Xue Kirita, Yuhei Morris, Samantha A. Genome Biol Method High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are heritable, enabling cell populations to be tagged, pooled, and tracked over time in the same experimental replicate. We demonstrate the utility of CellTag Indexing by sequencing transcriptomes using a variety of cell types, including long-term tracking of cell engraftment and differentiation in vivo. Together, this presents CellTag Indexing as a broadly applicable genetic multiplexing tool that is complementary with existing single-cell technologies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1699-y) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-09 /pmc/articles/PMC6509836/ /pubmed/31072405 http://dx.doi.org/10.1186/s13059-019-1699-y Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Guo, Chuner
Kong, Wenjun
Kamimoto, Kenji
Rivera-Gonzalez, Guillermo C.
Yang, Xue
Kirita, Yuhei
Morris, Samantha A.
CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
title CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
title_full CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
title_fullStr CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
title_full_unstemmed CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
title_short CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
title_sort celltag indexing: genetic barcode-based sample multiplexing for single-cell genomics
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509836/
https://www.ncbi.nlm.nih.gov/pubmed/31072405
http://dx.doi.org/10.1186/s13059-019-1699-y
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