Protocol to study the inheritance and propagation of non-genetically encoded states using barcode decay lineage tracing
Summary: Here, we present a protocol to perform barcode decay lineage tracing followed by single-cell transcriptome analysis (BdLT-Seq). We describe steps for BdLT-Seq experimental design, building barcoded episome reporters, performing episome transfection, and barcode retrieval. We then describe p...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-03-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723007761 |
| _version_ | 1797365608624422912 |
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| author | Yelyzaveta Shlyakhtina Bianca Bloechl Katherine L. Moran Maximiliano M. Portal |
| author_facet | Yelyzaveta Shlyakhtina Bianca Bloechl Katherine L. Moran Maximiliano M. Portal |
| author_sort | Yelyzaveta Shlyakhtina |
| collection | DOAJ |
| description | Summary: Here, we present a protocol to perform barcode decay lineage tracing followed by single-cell transcriptome analysis (BdLT-Seq). We describe steps for BdLT-Seq experimental design, building barcoded episome reporters, performing episome transfection, and barcode retrieval. We then describe procedures for sequencing library construction while providing options for sample multiplexing and data analysis. This BdLT-Seq technique enables the assessment of clonal evolution in a directional manner while preserving isogeneity, thus allowing the comparison of non-genetic molecular features between isogenic cell lineages.For complete details on the use and execution of this protocol, please refer to Shlyakhtina et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-08T16:51:23Z |
| format | Article |
| id | doaj.art-bd6ed260d81147a9b580e810e436c877 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-08T16:51:23Z |
| publishDate | 2024-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-bd6ed260d81147a9b580e810e436c8772024-01-05T04:25:13ZengElsevierSTAR Protocols2666-16672024-03-0151102809Protocol to study the inheritance and propagation of non-genetically encoded states using barcode decay lineage tracingYelyzaveta Shlyakhtina0Bianca Bloechl1Katherine L. Moran2Maximiliano M. Portal3Cell Plasticity & Epigenetics Lab, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK; Cell Plasticity & Epigenetics Lab, Cancer Research UK – Cancer Research UK Scotland Institute, The University of Glasgow, Glasgow G61 1BD, UKCell Plasticity & Epigenetics Lab, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK; Cell Plasticity & Epigenetics Lab, Cancer Research UK – Cancer Research UK Scotland Institute, The University of Glasgow, Glasgow G61 1BD, UKCell Plasticity & Epigenetics Lab, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UKCell Plasticity & Epigenetics Lab, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK; Cell Plasticity & Epigenetics Lab, Cancer Research UK – Cancer Research UK Scotland Institute, The University of Glasgow, Glasgow G61 1BD, UK; Corresponding authorSummary: Here, we present a protocol to perform barcode decay lineage tracing followed by single-cell transcriptome analysis (BdLT-Seq). We describe steps for BdLT-Seq experimental design, building barcoded episome reporters, performing episome transfection, and barcode retrieval. We then describe procedures for sequencing library construction while providing options for sample multiplexing and data analysis. This BdLT-Seq technique enables the assessment of clonal evolution in a directional manner while preserving isogeneity, thus allowing the comparison of non-genetic molecular features between isogenic cell lineages.For complete details on the use and execution of this protocol, please refer to Shlyakhtina et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723007761Cell BiologyGenomicsMolecular BiologySingle Cell |
| spellingShingle | Yelyzaveta Shlyakhtina Bianca Bloechl Katherine L. Moran Maximiliano M. Portal Protocol to study the inheritance and propagation of non-genetically encoded states using barcode decay lineage tracing STAR Protocols Cell Biology Genomics Molecular Biology Single Cell |
| title | Protocol to study the inheritance and propagation of non-genetically encoded states using barcode decay lineage tracing |
| title_full | Protocol to study the inheritance and propagation of non-genetically encoded states using barcode decay lineage tracing |
| title_fullStr | Protocol to study the inheritance and propagation of non-genetically encoded states using barcode decay lineage tracing |
| title_full_unstemmed | Protocol to study the inheritance and propagation of non-genetically encoded states using barcode decay lineage tracing |
| title_short | Protocol to study the inheritance and propagation of non-genetically encoded states using barcode decay lineage tracing |
| title_sort | protocol to study the inheritance and propagation of non genetically encoded states using barcode decay lineage tracing |
| topic | Cell Biology Genomics Molecular Biology Single Cell |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723007761 |
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