DOI: https://doi.org/10.1159/000529376
Chicken Cell Atlas: Science and DeSci
DOI:
https://doi.org/10.51094/jxiv.182Keywords:
single-cell RNA sequencing, cell atlas, transcriptome, proteome, multimodal integration, decentralized scienceAbstract
The chicken cell atlas project aims to chart the types and properties of all chicken cells across all organs and tissues, build a reference map of the mature and developing chicken bodies, and provide the resources for studying the biology of this species. It will potentially become an international collaboration among many researchers. This project will be useful for understanding the basic biology of chicken and other birds. The atlas will include spatial and temporal single-cell data on multiple modalities such as transcriptome, proteome, epigenome, glycome, metabolome, electrophysiology, morphology, and connectome. The possibility of establishing a decentralized organization based on cutting-edge crypto-technologies is discussed to create an armamentarium and organize research resources and incentives.
Downloads *Displays the aggregated results up to the previous day.
References
Alfieri JM, Wang G, Jonika MM, Gill CA, Blackmon H, Athrey GN. A Primer for Single-Cell Sequencing in Non-Model Organisms. Genes (Basel). 2022;13(2):380.
Armand EJ, Li J, Xie F, Luo C, Mukamel EA. Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes. Neuron. 2021;109(1):11-26.
Burt DW. Emergence of the Chicken as a Model Organism: Implications for Agriculture and Biology. Poult. Sci. 2007; 86(7):1460–1471.
Chen A, Liao S, Cheng M, Ma K, Wu L, Lai Y, Qiu X, Yang J, Xu J, Hao S, Wang X, Lu H, Chen X, Liu X, Huang X, Li Z, Hong Y, Jiang Y, Peng J, Liu S, Shen M, Liu C, Li Q, Yuan Y, Wei X, Zheng H, Feng W, Wang Z, Liu Y, Wang Z, Yang Y, Xiang H, Han L, Qin B, Guo P, Lai G, Muñoz-Cánoves P, Maxwell PH, Thiery JP, Wu QF, Zhao F, Chen B, Li M, Dai X, Wang S, Kuang H, Hui J, Wang L, Fei JF, Wang O, Wei X, Lu H, Wang B, Liu S, Gu Y, Ni M, Zhang W, Mu F, Yin Y, Yang H, Lisby M, Cornall RJ, Mulder J, Uhlén M, Esteban MA, Li Y, Liu L, Xu X, Wang J. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell. 2022;185(10):1777-1792.e21.
Cho NH, Cheveralls KC, Brunner AD, Kim K, Michaelis AC, Raghavan P, Kobayashi H, Savy L, Li JY, Canaj H, Kim JYS, Stewart EM, Gnann C, McCarthy F, Cabrera JP, Brunetti RM, Chhun BB, Dingle G, Hein MY, Huang B, Mehta SB, Weissman JS, Gómez-Sjöberg R, Itzhak DN, Royer LA, Mann M, Leonetti MD. OpenCell: Endogenous tagging for the cartography of human cellular organization. Science. 2022; 375(6585):eabi6983.
Clinton M, Haines L, Belloir B, McBride D. Sexing chick embryos: a rapid and simple protocol. Br Poult Sci. 2001; 42(1):134-138.
Colquitt BM, Merullo DP, Konopka G, Roberts TF, Brainard MS. Cellular transcriptomics reveals evolutionary identities of songbird vocal circuits. Science. 2021;371(6530):eabd9704.
De Lima JE, Blavet C, Bonnin MA, Hirsinger E, Comai G, Yvernogeau L, Delfini MC, Bellenger L, Mella S, Nassari S, et al. Unexpected contribution of fibroblasts to muscle lineage as a mechanism for limb muscle patterning. Nat. Commun. 2021;12(1):3851.
Eraslan G, Drokhlyansky E, Anand S, Fiskin E, Subramanian A, Slyper M, Wang J, Van Wittenberghe N, Rouhana JM, Waldman J, Ashenberg O, Lek M, Dionne D, Win TS, Cuoco MS, Kuksenko O, Tsankov AM, Branton PA, Marshall JL, Greka A, Getz G, Segrè AV, Aguet F, Rozenblatt-Rosen O, Ardlie KG, Regev A. Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Science. 2022;376(6594):eabl4290.
Estermann MA, Williams S, Hirst CE, Roly ZY, Serralbo O, Adhikari D, Powell D, Major AT, Smith CA. Insights into Gonadal Sex Differentiation Provided by Single-Cell Transcriptomics in the Chicken Embryo. Cell Rep. 2020;31(1):107491.
Feregrino C, Sacher F, Parnas O, Tschopp P. A single-cell transcriptomic atlas of the developing chicken limb. BMC Genom. 2019;20(1):401.
Gandhi S, Hutchins EJ, Maruszko K, Park JH, Thomson M, Bronner ME. Bimodal function of chromatin remodeler Hmga1 in neural crest induction and Wnt-dependent emigration. eLife. 2020;9:e57779.
Guillot C, Djeffal Y, Michaut A, Rabe B, Pourquié O. Dynamics of primitive streak regression controls the fate of neuromesodermal progenitors in the chicken embryo. eLife. 2021;10:e64819.
Guo S, Zhang C, Le A. The limitless applications of single-cell metabolomics. Curr Opin Biotechnol. 2021;71:115-122.
Hamburg S. Call to join the decentralized science movement. Nature. 2021; 600(7888):221.
Hamburger V, Hamilton HL. A series of normal stages in the development of the chick embryo. J. Morphol. 1951; 88(1), 49–92.
Haniffa M, Taylor, D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Gray Camp J, Chédotal A, Copp A. et al. A roadmap for the Human Developmental Cell Atlas. Nature 2021; 597(7875):196–205.
Hoang T, Wang J, Boyd P, Wang F, Santiago C, Jiang L, Yoo S, Lahne M, Todd LJ, Jia M, Saez C, Keuthan C, Palazzo I, Squires N, Campbell WA, Rajaii F, Parayil T, Trinh V, Kim DW, Wang G, Campbell LJ, Ash J, Fischer AJ, Hyde DR, Qian J, Blackshaw S. Gene regulatory networks controlling vertebrate retinal regeneration. Science. 2020;370(6519):eabb8598.
HuBMAP Consortium. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. 2019;574(7777):187-192.
Janesick A., Scheibinger M., Benkafadar N., Kirti S., Ellwanger D.C., Heller S. Cell-type identity of the avian cochlea. Cell Rep. 2021;34(12):108900.
Kim DW, Place E, Chinnaiya K, Manning E, Sun C, Dai W, Groves I, Ohyama K, Burbridge S, Placzek M, Blackshaw S. Single-cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamic-like progenitors. Cell Rep. 2022;38(3):110251.
Lee BR, Budzillo A, Hadley K, Miller JA, Jarsky T, Baker K, Hill D, Kim L, Mann R, Ng L, Oldre A, Rajanbabu R, Trinh J, Vargas S, Braun T, Dalley RA, Gouwens NW, Kalmbach BE, Kim TK, Smith KA, Soler-Llavina G, Sorensen S, Tasic B, Ting JT, Lein E, Zeng H, Murphy GJ, Berg J. Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization. eLife. 2021;10:e65482.
Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David FPA, et al. Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science. 2022;375(6584):eabk2432.
Li J, Xing S, Zhao G, Zheng M, Yang X, Sun J, Wen J, Liu R. Identification of diverse cell populations in skeletal muscles and biomarkers for intramuscular fat of chicken by single-cell RNA sequencing. BMC Genom. 2020;21(1):752.
Lindeboom RGH, Regev A, Teichmann SA. Towards a Human Cell Atlas: Taking Notes from the Past. Trends Genet. 2021;37(7):625-630.
Luecken MD, Theis FJ. Current best practices in single-cell RNA-seq analysis: a tutorial. Mol Syst Biol. 2019;15(6):e8746.
Mantri M, Scuderi GJ, Abedini-Nassab R, Wang MFZ, McKellar D, Shi H, Grodner B, Butcher JT, De Vlaminck I. Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis. Nat Commun. 2021;12(1):1771.
Moffitt JR, Lundberg E, Heyn H. The emerging landscape of spatial profiling technologies. Nat Rev Genet. 2022 Jul 20.
Morrison J.A., McLennan R., Wolfe L.A., Gogol M.M., Meier S., McKinney M.C., Teddy J.M., Holmes L., Semerad C.L., Box A.C., et al. Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions. eLife. 2017;6:e28415.
Morrison JA, Box AC, McKinney MC, McLennan R, Kulesa PM. Quantitative single cell gene expression profiling in the avian embryo. Dev Dyn. 2015;244(6):774-784.
Moses L, Pachter L. Museum of spatial transcriptomics. Nat Methods. 2022;19(5):534-546.
Mund A, Brunner AD, Mann M. Unbiased spatial proteomics with single-cell resolution in tissues. Mol Cell. 2022;82(12):2335-2349.
Núñez-León D, Aguirre-Fernández G, Steiner A, Nagashima H, Jensen P, Stoeckli E, Schneider RA, Sánchez-Villagra MR. Morphological diversity of integumentary traits in fowl domestication: Insights from disparity analysis and embryonic development. Dev Dyn. 2019;248(11):1044-1058.
Palla G, Fischer DS, Regev A, Theis FJ. Spatial components of molecular tissue biology. Nat Biotechnol. 2022;40(3):308-318.
Qu X, Li X, Li Z, Liao M, Dai M. Chicken Peripheral Blood Mononuclear Cells Response to Avian Leukosis Virus Subgroup J Infection Assessed by Single-Cell RNA Sequencing. Front Microbiol. 2022;13:800618.
Rao A, Barkley D, França GS, Yanai I. Exploring tissue architecture using spatial transcriptomics. Nature. 2021;596(7871):211-220.
Rengaraj D, Cha DG, Lee HJ, Lee KY, Choi YH, Jung KM, Kim YM, Choi HJ, Choi HJ, Yoo E, Woo SJ, Park JS, Park KJ, Kim JK, Han JY. Dissecting chicken germ cell dynamics by combining a germ cell tracing transgenic chicken model with single-cell RNA sequencing. Comput Struct Biotechnol J. 2022;20:1654-1669.
Saunders A, Huang KW, Vondrak C, Hughes C, Smolyar K, Sen H, Philson AC, Nemesh J, Wysoker A, Kashin S, Sabatini BL, McCarroll SA. Ascertaining cells’ synaptic connections and RNA expression simultaneously with massively barcoded rabies virus libraries
bioRxiv 2021.09.06.459177.
Stern CD. The chick; A great model system becomes even greater. Dev Cell. 2005; 8(1), 9–17.
Stuart T, Satija R. Integrative single-cell analysis. Nat Rev Genet. 2019;20(5):257-272.
Sun YC, Chen X, Fischer S, Lu S, Zhan H, Gillis J, Zador AM. Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections. Nat Neurosci. 2021:873-885.
Tabula Muris Consortium. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 2018, 562(7727), 367–372.
Tabula Sapiens Consortium. The Tabula Sapiens: a multiple-organ, single-cell transcriptomic atlas of humans. Science 2022;376(6594):eabl4896.
Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, Poff A, Basavaraju M, Rafi I, Yemini E, Cook SJ, Abrams A, Vidal B, Cros C, Tavazoie S, Sestan N, Hammarlund M, Hobert O, Miller DM 3rd. Molecular topography of an entire nervous system. Cell. 2021;184(16):4329-4347..
Tegla MGG, Buenaventura DF, Kim DY, Thakurdin C, Gonzalez KC, Emerson MM. OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification. eLife. 2020;9:e54279.
Vermillion KL, Bacher R, Tannenbaum AP, Swanson S, Jiang P, Chu LF, Stewart R, Thomson JA, Vereide DT. Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes. Dev Biol. 2018;439(1):30-41.
Williams RM, Lukoseviciute M, Sauka-Spengler T, Bronner ME. Single-cell atlas of early chick development reveals gradual segregation of neural crest lineage from the neural plate border during neurulation. eLife. 2022;11:e74464.
Yamagata M, Yan W, Sanes JR. A cell atlas of the chick retina based on single-cell transcriptomics. eLife. 2021;10:e63907.
Yamagata M, Sanes JR. CRISPR-mediated Labeling of Cells in Chick Embryos Based on Selectively Expressed Genes. Bio Protoc. 2021;11(15):e4105.
Yamagata M. Towards Tabula Gallus. Int J Mol Sci. 2022;23(2):613.
Zeng H. What is a cell type and how to define it? Cell. 2022;185(15):2739-2755.
Zhang J, Lv C, Mo C, Liu M, Wan Y, Li J, Wang Y. Single-cell RNA sequencing analysis of chicken anterior pituitary: A bird’s-eye view on vertebrate pituitary. Front. Physiol. 2021;12:562817.
Zhuang X. Spatially resolved single-cell genomics and transcriptomics by imaging.
Nat. Methods. 2021;18(1):18-22
Downloads
Posted
Submitted: 2022-10-06 03:31:49 UTC
Published: 2022-10-11 05:22:11 UTC
License
Copyright (c) 2022
Masahito Yamagata
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.