9 papers · ranked by Valyu relevance
Givanna H. Putri, Nichelle Pires, Nadia M. Davidson, Catherine Blyth + 3 more
The study of clonal dynamics has significantly advanced our understanding of cellular heterogeneity and lineage trajectories. With recent developments in lineage-tracing protocols such as ClonMapper or SPLINTR, which combine DNA barcoding with single-cell RNA sequencing (scRNA-seq), biologists can trace the lineage and…
Grant Kinsler, Caitlin Fagan, Haiyin Li, Jessica Kaster + 7 more
We report a cellular barcoding strategy, SpaceBar, that enables simultaneous clone tracing and spatial transcriptomics profiling. Our approach uses a library of 96 synthetic barcode sequences that can be robustly detected by imaging based spatial transcriptomics (seqFISH), delivered such that each cell is labeled with…
Roberto Rota, Elizabeth Flittner, Matteo Tartagni, Marwane Bourdim + 16 more
Experimental dissection of clonal dynamics in complex tissues requires barcoding systems that are scalable, compatible with different analytical platforms, providing phenotypic and spatial resolution. Here we introduce X-CODE, a dual-expressed RNA barcoding system designed to enable high-complexity clonal tracking…
Sayaka Miura, Karen Gomez, Oscar Murillo, Louise A Huuki + 3 more
Analyses of data generated from bulk sequencing of tumors have revealed extensive genomic heterogeneity within patients. Many computational methods have been developed to enable the inference of genotypes of tumor cell populations (clones) from bulk sequencing data. However, the relative and absolute accuracy of…
Daniel Postrach, Colin E. J. Pritchard, Larissa Frank, Tom van Leeuwen + 4 more
Tracing the fate of individual cells and their progeny remains a challenging task. While imaging-based fate-mapping provides spatial information, it generally lacks complexity due to limited label diversity, resulting in diminished capture of comprehensive lineages and fate maps. Here, we introduce ‘Polytope’, an…
Soh Ishiguro, Kana Ishida, Rina C. Sakata, Hideto Mori + 20 more
Clonal heterogeneity underlies diverse biological processes, including cancer progression, cell differentiation, and microbial evolution. Cell tagging strategies with DNA barcodes have recently enabled analysis of clone size dynamics and clone-restricted transcriptomic landscapes of heterogeneous populations. However…
Liyang Fei, Jovana Maksimovic, Alicia Oshlack
Tracking the clonal composition of pools of cells as they differentiate or evolve can reveal important features of development and clonal evolution in fields such as stem cell research and cancer. A variety of new single-cell lineage tracing technologies now allow us to track progeny cells back to their original…
Yevhen Akimov, Daria Bulanova, Sanna Timonen, Krister Wennerberg + 1 more
Cellular DNA barcoding has become a popular approach to study heterogeneity of cell populations and to identify lineages with differential response to cellular stimuli. However, there is a lack of reliable methods for statistical inference of differentially responding lineages. Here, we used mixtures of DNA-barcoded…
Diego A. Espinoza, Ryland D. Mortlock, Samson J. Koelle, Chuanfeng Wu + 1 more
Clonal tracking methods provide quantitative insights into the cellular output of genetically labelled progenitor cells across time and cellular compartments. However, the absence of a toolbox by which to interrogate these data has precluded the development of standardized analytical frameworks within the field. Thus…