Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies
Advances in single-cell sequencing technologies have provided novel insights into the dynamics of gene expression and cellular heterogeneity within tissues and have enabled the construction of transcriptomic cell atlases. However, linking anatomical information to transcriptomic data and positively...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2025-02-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/88334 |
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| _version_ | 1832095839753863168 |
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| author | Jorge Blanco Mendana Margaret Donovan Lindsey Gengelbach O'Brien Benjamin Auch John Garbe Daryl M Gohl |
| author_facet | Jorge Blanco Mendana Margaret Donovan Lindsey Gengelbach O'Brien Benjamin Auch John Garbe Daryl M Gohl |
| author_sort | Jorge Blanco Mendana |
| collection | DOAJ |
| description | Advances in single-cell sequencing technologies have provided novel insights into the dynamics of gene expression and cellular heterogeneity within tissues and have enabled the construction of transcriptomic cell atlases. However, linking anatomical information to transcriptomic data and positively identifying the cell types that correspond to gene expression clusters in single-cell sequencing data sets remains a challenge. We describe a straightforward genetic barcoding approach that takes advantage of the powerful genetic tools in Drosophila to allow in vivo tagging of defined cell populations. This method, called Targeted Genetically-Encoded Multiplexing (TaG-EM), involves inserting a DNA barcode just upstream of the polyadenylation site in a Gal4-inducible UAS-GFP construct so that the barcode sequence can be read out during single-cell sequencing, labeling a cell population of interest. By creating many such independently barcoded fly strains, TaG-EM enables positive identification of cell types in cell atlas projects, identification of multiplet droplets, and barcoding of experimental timepoints, conditions, and replicates. Furthermore, we demonstrate that TaG-EM barcodes can be read out using next-generation sequencing to facilitate population-scale behavioral measurements. Thus, TaG-EM has the potential to enable large-scale behavioral screens in addition to improving the ability to multiplex and reliably annotate single-cell transcriptomic experiments. |
| format | Article |
| id | doaj-art-9b68712cd2c24723b0e991a6296479d3 |
| institution | Kabale University |
| issn | 2050-084X |
| language | English |
| publishDate | 2025-02-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj-art-9b68712cd2c24723b0e991a6296479d32025-02-05T16:29:18ZengeLife Sciences Publications LtdeLife2050-084X2025-02-011210.7554/eLife.88334Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studiesJorge Blanco Mendana0Margaret Donovan1https://orcid.org/0009-0007-1779-4459Lindsey Gengelbach O'Brien2https://orcid.org/0009-0007-5423-7387Benjamin Auch3John Garbe4Daryl M Gohl5https://orcid.org/0000-0002-4434-2788University of Minnesota Genomics Center, Minneapolis, Minneapolis, United StatesUniversity of Minnesota Genomics Center, Minneapolis, Minneapolis, United StatesUniversity of Minnesota Genomics Center, Minneapolis, Minneapolis, United StatesUniversity of Minnesota Genomics Center, Minneapolis, Minneapolis, United StatesUniversity of Minnesota Genomics Center, Minneapolis, Minneapolis, United StatesUniversity of Minnesota Genomics Center, Minneapolis, Minneapolis, United States; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United StatesAdvances in single-cell sequencing technologies have provided novel insights into the dynamics of gene expression and cellular heterogeneity within tissues and have enabled the construction of transcriptomic cell atlases. However, linking anatomical information to transcriptomic data and positively identifying the cell types that correspond to gene expression clusters in single-cell sequencing data sets remains a challenge. We describe a straightforward genetic barcoding approach that takes advantage of the powerful genetic tools in Drosophila to allow in vivo tagging of defined cell populations. This method, called Targeted Genetically-Encoded Multiplexing (TaG-EM), involves inserting a DNA barcode just upstream of the polyadenylation site in a Gal4-inducible UAS-GFP construct so that the barcode sequence can be read out during single-cell sequencing, labeling a cell population of interest. By creating many such independently barcoded fly strains, TaG-EM enables positive identification of cell types in cell atlas projects, identification of multiplet droplets, and barcoding of experimental timepoints, conditions, and replicates. Furthermore, we demonstrate that TaG-EM barcodes can be read out using next-generation sequencing to facilitate population-scale behavioral measurements. Thus, TaG-EM has the potential to enable large-scale behavioral screens in addition to improving the ability to multiplex and reliably annotate single-cell transcriptomic experiments.https://elifesciences.org/articles/88334next-generation sequencingsingle-cell transcriptomicsgenetic barcodingbehavior |
| spellingShingle | Jorge Blanco Mendana Margaret Donovan Lindsey Gengelbach O'Brien Benjamin Auch John Garbe Daryl M Gohl Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies eLife next-generation sequencing single-cell transcriptomics genetic barcoding behavior |
| title | Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies |
| title_full | Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies |
| title_fullStr | Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies |
| title_full_unstemmed | Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies |
| title_short | Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies |
| title_sort | deterministic genetic barcoding for multiplexed behavioral and single cell transcriptomic studies |
| topic | next-generation sequencing single-cell transcriptomics genetic barcoding behavior |
| url | https://elifesciences.org/articles/88334 |
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