BdLT-Seq as a barcode decay-based method to unravel lineage-linked transcriptome plasticity
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-023-36744-1
Download full text from publisher
References listed on IDEAS
- Sydney M. Shaffer & Margaret C. Dunagin & Stefan R. Torborg & Eduardo A. Torre & Benjamin Emert & Clemens Krepler & Marilda Beqiri & Katrin Sproesser & Patricia A. Brafford & Min Xiao & Elliott Eggan , 2017. "Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance," Nature, Nature, vol. 546(7658), pages 431-435, June.
- Alex Sigal & Ron Milo & Ariel Cohen & Naama Geva-Zatorsky & Yael Klein & Yuvalal Liron & Nitzan Rosenfeld & Tamar Danon & Natalie Perzov & Uri Alon, 2006. "Variability and memory of protein levels in human cells," Nature, Nature, vol. 444(7119), pages 643-646, November.
- Rowan D Brackston & Eszter Lakatos & Michael P H Stumpf, 2018. "Transition state characteristics during cell differentiation," PLOS Computational Biology, Public Library of Science, vol. 14(9), pages 1-24, September.
- Brent A. Biddy & Wenjun Kong & Kenji Kamimoto & Chuner Guo & Sarah E. Waye & Tao Sun & Samantha A. Morris, 2018. "Single-cell mapping of lineage and identity in direct reprogramming," Nature, Nature, vol. 564(7735), pages 219-224, December.
- Anna Alemany & Maria Florescu & Chloé S. Baron & Josi Peterson-Maduro & Alexander van Oudenaarden, 2018. "Whole-organism clone tracing using single-cell sequencing," Nature, Nature, vol. 556(7699), pages 108-112, April.
- Michelle M. Chan & Zachary D. Smith & Stefanie Grosswendt & Helene Kretzmer & Thomas M. Norman & Britt Adamson & Marco Jost & Jeffrey J. Quinn & Dian Yang & Matthew G. Jones & Alex Khodaverdian & Nir , 2019. "Molecular recording of mammalian embryogenesis," Nature, Nature, vol. 570(7759), pages 77-82, June.
- Hannah H. Chang & Martin Hemberg & Mauricio Barahona & Donald E. Ingber & Sui Huang, 2008. "Transcriptome-wide noise controls lineage choice in mammalian progenitor cells," Nature, Nature, vol. 453(7194), pages 544-547, May.
- Angela Oliveira Pisco & Amy Brock & Joseph Zhou & Andreas Moor & Mitra Mojtahedi & Dean Jackson & Sui Huang, 2013. "Non-Darwinian dynamics in therapy-induced cancer drug resistance," Nature Communications, Nature, vol. 4(1), pages 1-11, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Xinhai Pan & Hechen Li & Pranav Putta & Xiuwei Zhang, 2023. "LinRace: cell division history reconstruction of single cells using paired lineage barcode and gene expression data," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Jun Dai & Shuyu Zheng & Matías M. Falco & Jie Bao & Johanna Eriksson & Sanna Pikkusaari & Sofia Forstén & Jing Jiang & Wenyu Wang & Luping Gao & Fernando Perez-Villatoro & Olli Dufva & Khalid Saeed & , 2024. "Tracing back primed resistance in cancer via sister cells," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- A. S. Eisele & M. Tarbier & A. A. Dormann & V. Pelechano & D. M. Suter, 2024. "Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Guillaume Harmange & Raúl A. Reyes Hueros & Dylan L. Schaff & Benjamin Emert & Michael Saint-Antoine & Laura C. Kim & Zijian Niu & Shivani Nellore & Mitchell E. Fane & Gretchen M. Alicea & Ashani T. W, 2023. "Disrupting cellular memory to overcome drug resistance," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Suzanne Gaudet & Sabrina L Spencer & William W Chen & Peter K Sorger, 2012. "Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis," PLOS Computational Biology, Public Library of Science, vol. 8(4), pages 1-15, April.
- Humberto Contreras-Trujillo & Jiya Eerdeng & Samir Akre & Du Jiang & Jorge Contreras & Basia Gala & Mary C. Vergel-Rodriguez & Yeachan Lee & Aparna Jorapur & Areen Andreasian & Lisa Harton & Charles S, 2021. "Deciphering intratumoral heterogeneity using integrated clonal tracking and single-cell transcriptome analyses," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
- Damien G Hicks & Terence P Speed & Mohammed Yassin & Sarah M Russell, 2019. "Maps of variability in cell lineage trees," PLOS Computational Biology, Public Library of Science, vol. 15(2), pages 1-32, February.
- Gautam Dey & Gagan D Gupta & Balaji Ramalingam & Mugdha Sathe & Satyajit Mayor & Mukund Thattai, 2014. "Exploiting Cell-To-Cell Variability To Detect Cellular Perturbations," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-10, March.
- Franziska Haderk & Yu-Ting Chou & Lauren Cech & Celia Fernández-Méndez & Johnny Yu & Victor Olivas & Ismail M. Meraz & Dora Barbosa Rabago & D. Lucas Kerr & Carlos Gomez & David V. Allegakoen & Juan G, 2024. "Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Singh, Abhyudai & Vahdat, Zahra & Xu, Zikai, 2019. "Time-triggered stochastic hybrid systems with two timer-dependent resets," OSF Preprints u8fzg, Center for Open Science.
- Xue Zhang & Shishir M. Pant & Cecily C. Ritch & Hsin-Yao Tang & Hongguang Shao & Harsh Dweep & Yao-Yu Gong & Rebekah Brooks & Patricia Brafford & Adam J. Wolpaw & Yool Lee & Ashani Weeraratna & Amita , 2024. "Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Linghua Zhou & Yong Shen & Libo Jiang & Danni Yin & Jingxin Guo & Hui Zheng & Hao Sun & Rongling Wu & Yunqian Guo, 2015. "Systems Mapping for Hematopoietic Progenitor Cell Heterogeneity," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-18, May.
- Monica T. Dayao & Maigan Brusko & Clive Wasserfall & Ziv Bar-Joseph, 2022. "Membrane marker selection for segmenting single cell spatial proteomics data," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
- Heike Chauvistré & Batool Shannan & Sheena M. Daignault-Mill & Robert J. Ju & Daniel Picard & Stefanie Egetemaier & Renáta Váraljai & Christine S. Gibhardt & Antonio Sechi & Farnusch Kaschani & Oliver, 2022. "Persister state-directed transitioning and vulnerability in melanoma," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
- Jonathan Liu & Donald Hansen & Elizabeth Eck & Yang Joon Kim & Meghan Turner & Simon Alamos & Hernan Garcia, 2021. "Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage," PLOS Computational Biology, Public Library of Science, vol. 17(5), pages 1-26, May.
- Angélique Richard & Loïs Boullu & Ulysse Herbach & Arnaud Bonnafoux & Valérie Morin & Elodie Vallin & Anissa Guillemin & Nan Papili Gao & Rudiyanto Gunawan & Jérémie Cosette & Ophélie Arnaud & Jean-Ja, 2016. "Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process," PLOS Biology, Public Library of Science, vol. 14(12), pages 1-35, December.
- Alok Maity & Roy Wollman, 2020. "Information transmission from NFkB signaling dynamics to gene expression," PLOS Computational Biology, Public Library of Science, vol. 16(8), pages 1-16, August.
- Jaishree Tripathi & Lei Zhu & Sourav Nayak & Michal Stoklasa & Zbynek Bozdech, 2022. "Stochastic expression of invasion genes in Plasmodium falciparum schizonts," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Arpiar Saunders & Kee Wui Huang & Cassandra Vondrak & Christina Hughes & Karina Smolyar & Harsha Sen & Adrienne C. Philson & James Nemesh & Alec Wysoker & Seva Kashin & Bernardo L. Sabatini & Steven A, 2022. "Ascertaining cells’ synaptic connections and RNA expression simultaneously with barcoded rabies virus libraries," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Tsuchiya, Masa & Selvarajoo, Kumar & Piras, Vincent & Tomita, Masaru & Giuliani, Alessandro, 2009. "Local and global responses in complex gene regulation networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 388(8), pages 1738-1746.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36744-1. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.