10 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…
Qiuchen Guo, Milos Spasic, Adam Maynard, Gregory J. Goreczny + 3 more
Over recent decades, cell lineage tracing, clonal analyses, molecular barcoding, and single cell “omic” analysis methods have proven to be valuable tools for research and discovery. Here, we report a clonal molecular barcoding method, which we term SunCatcher, that enables longitudinal tracking and retrieval of live…
Lei Yu, John J. Stachowicz, Katie DuBois, Thorsten B. H. Reusch
Clonal reproduction, the production of asexual modular units with the ability to live independently under multicellularity, is a very common life history. Genetic markers have been widely used to detect clonemates tracing back to a single sexual event. However, the currently available methods cannot work in cases where…
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…
Lachlan Cain, Anna S Trigos
Single-cell analyses of cancer typically begin by identifying distinct populations of cancer cells by unsupervised clustering. However, in many cases this clustering is explained simply by differences in DNA copy number, which affects the interpretation of differential expression results and tumour heterogeneity…
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…
Shalini Raj Unnikandam Veettil, Joanna Donatelli, Geetansh Kalra, Constanza Verónica Ljubetic San Martín + 9 more
The generation of clonal CHO cell lines is foundational to biologics manufacturing; however, labor-intensive cell culture workflows predominate in the field. We created the CLAIRE (Cell Line AI Recognition and Evaluation) tool to streamline end-to-end cell line development by integrating deep-learning image analysis…