Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis. / Liu, Chang; Li, Rui; Li, Young; Lin, Xiumei; Zhao, Kaichen; Liu, Qun; Wang, Shuowen; Yang, Xueqian; Shi, Xuyang; Ma, Yuting; Pei, Chenyu; Wang, Hui; Bao, Wendai; Hui, Junhou; Yang, Tao; Xu, Zhicheng; Lai, Tingting; Berberoglu, Michael Arman; Sahu, Sunil Kumar; Esteban, Miguel A.; Ma, Kailong; Fan, Guangyi; Li, Yuxiang; Liu, Shiping; Chen, Ao; Xu, Xun; Dong, Zhiqiang; Liu, Longqi.

In: Developmental Cell, Vol. 57, No. 10, 2022, p. 1284-1298.e5.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Liu, C, Li, R, Li, Y, Lin, X, Zhao, K, Liu, Q, Wang, S, Yang, X, Shi, X, Ma, Y, Pei, C, Wang, H, Bao, W, Hui, J, Yang, T, Xu, Z, Lai, T, Berberoglu, MA, Sahu, SK, Esteban, MA, Ma, K, Fan, G, Li, Y, Liu, S, Chen, A, Xu, X, Dong, Z & Liu, L 2022, 'Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis', Developmental Cell, vol. 57, no. 10, pp. 1284-1298.e5. https://doi.org/10.1016/j.devcel.2022.04.009

APA

Liu, C., Li, R., Li, Y., Lin, X., Zhao, K., Liu, Q., Wang, S., Yang, X., Shi, X., Ma, Y., Pei, C., Wang, H., Bao, W., Hui, J., Yang, T., Xu, Z., Lai, T., Berberoglu, M. A., Sahu, S. K., ... Liu, L. (2022). Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis. Developmental Cell, 57(10), 1284-1298.e5. https://doi.org/10.1016/j.devcel.2022.04.009

Vancouver

Liu C, Li R, Li Y, Lin X, Zhao K, Liu Q et al. Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis. Developmental Cell. 2022;57(10):1284-1298.e5. https://doi.org/10.1016/j.devcel.2022.04.009

Author

Liu, Chang ; Li, Rui ; Li, Young ; Lin, Xiumei ; Zhao, Kaichen ; Liu, Qun ; Wang, Shuowen ; Yang, Xueqian ; Shi, Xuyang ; Ma, Yuting ; Pei, Chenyu ; Wang, Hui ; Bao, Wendai ; Hui, Junhou ; Yang, Tao ; Xu, Zhicheng ; Lai, Tingting ; Berberoglu, Michael Arman ; Sahu, Sunil Kumar ; Esteban, Miguel A. ; Ma, Kailong ; Fan, Guangyi ; Li, Yuxiang ; Liu, Shiping ; Chen, Ao ; Xu, Xun ; Dong, Zhiqiang ; Liu, Longqi. / Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis. In: Developmental Cell. 2022 ; Vol. 57, No. 10. pp. 1284-1298.e5.

Bibtex

@article{f032e4ac98994cdf9ba5a35175dd3b5f,

title = "Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis",

abstract = "A major challenge in understanding vertebrate embryogenesis is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell-fate decisions. Here, we employed Stereo-seq to profile 91 zebrafish embryo sections covering six critical time points during the first 24 h of development, obtaining a total of 152,977 spots at a resolution of 10 × 10 × 15 μm3 (close to cellular size) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrated analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell-fate transitions and molecular changes during zebrafish embryogenesis. We further investigated the spatial distribution of ligand-receptor pairs and identified potentially important interactions during zebrafish embryo development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.",

keywords = "Animals, Embryo, Mammalian, Embryonic Development/genetics, Gene Expression Profiling, Gene Expression Regulation, Developmental, Transcriptome, Zebrafish/genetics",

author = "Chang Liu and Rui Li and Young Li and Xiumei Lin and Kaichen Zhao and Qun Liu and Shuowen Wang and Xueqian Yang and Xuyang Shi and Yuting Ma and Chenyu Pei and Hui Wang and Wendai Bao and Junhou Hui and Tao Yang and Zhicheng Xu and Tingting Lai and Berberoglu, {Michael Arman} and Sahu, {Sunil Kumar} and Esteban, {Miguel A.} and Kailong Ma and Guangyi Fan and Yuxiang Li and Shiping Liu and Ao Chen and Xun Xu and Zhiqiang Dong and Longqi Liu",

year = "2022",

doi = "10.1016/j.devcel.2022.04.009",

language = "English",

volume = "57",

pages = "1284--1298.e5",

journal = "Developmental Cell",

issn = "1534-5807",

publisher = "Cell Press",

number = "10",

}

RIS

TY - JOUR

T1 - Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

AU - Liu, Chang

AU - Li, Rui

AU - Li, Young

AU - Lin, Xiumei

AU - Zhao, Kaichen

AU - Liu, Qun

AU - Wang, Shuowen

AU - Yang, Xueqian

AU - Shi, Xuyang

AU - Ma, Yuting

AU - Pei, Chenyu

AU - Wang, Hui

AU - Bao, Wendai

AU - Hui, Junhou

AU - Yang, Tao

AU - Xu, Zhicheng

AU - Lai, Tingting

AU - Berberoglu, Michael Arman

AU - Sahu, Sunil Kumar

AU - Esteban, Miguel A.

AU - Ma, Kailong

AU - Fan, Guangyi

AU - Li, Yuxiang

AU - Liu, Shiping

AU - Chen, Ao

AU - Xu, Xun

AU - Dong, Zhiqiang

AU - Liu, Longqi

PY - 2022

Y1 - 2022

N2 - A major challenge in understanding vertebrate embryogenesis is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell-fate decisions. Here, we employed Stereo-seq to profile 91 zebrafish embryo sections covering six critical time points during the first 24 h of development, obtaining a total of 152,977 spots at a resolution of 10 × 10 × 15 μm3 (close to cellular size) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrated analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell-fate transitions and molecular changes during zebrafish embryogenesis. We further investigated the spatial distribution of ligand-receptor pairs and identified potentially important interactions during zebrafish embryo development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.

AB - A major challenge in understanding vertebrate embryogenesis is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell-fate decisions. Here, we employed Stereo-seq to profile 91 zebrafish embryo sections covering six critical time points during the first 24 h of development, obtaining a total of 152,977 spots at a resolution of 10 × 10 × 15 μm3 (close to cellular size) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrated analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell-fate transitions and molecular changes during zebrafish embryogenesis. We further investigated the spatial distribution of ligand-receptor pairs and identified potentially important interactions during zebrafish embryo development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.

KW - Animals

KW - Embryo, Mammalian

KW - Embryonic Development/genetics

KW - Gene Expression Profiling

KW - Gene Expression Regulation, Developmental

KW - Transcriptome

KW - Zebrafish/genetics

U2 - 10.1016/j.devcel.2022.04.009

DO - 10.1016/j.devcel.2022.04.009

M3 - Journal article

C2 - 35512701

VL - 57

SP - 1284-1298.e5

JO - Developmental Cell

JF - Developmental Cell

SN - 1534-5807

IS - 10

ER -

ID: 310559150

Department of Biology