Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

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

Standard

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. / Chen, Ao; Liao, Sha; Cheng, Mengnan; Ma, Kailong; Wu, Liang; Lai, Yiwei; Qiu, Xiaojie; Yang, Jin; Xu, Jiangshan; Hao, Shijie; Wang, Xin; Lu, Huifang; Chen, Xi; Liu, Xing; Huang, Xin; Li, Zhao; Hong, Yan; Jiang, Yujia; Peng, Jian; Liu, Shuai; Shen, Mengzhe; Liu, Chuanyu; Li, Quanshui; Yuan, Yue; Wei, Xiaoyu; Zheng, Huiwen; Feng, Weimin; Wang, Zhifeng; Liu, Yang; Wang, Zhaohui; Yang, Yunzhi; Xiang, Haitao; Han, Lei; Qin, Baoming; Guo, Pengcheng; Lai, Guangyao; Muñoz-Cánoves, Pura; Maxwell, Patrick H; Thiery, Jean Paul; Wu, Qing-Feng; Zhao, Fuxiang; Chen, Bichao; Li, Mei; Dai, Xi; Wang, Shuai; Kuang, Haoyan; Hui, Junhou; Wang, Liqun; Fei, Ji-Feng; Wang, Ou; Wei, Xiaofeng; Lu, Haorong; Wang, Bo; Liu, Shiping; Gu, Ying; Ni, Ming; Zhang, Wenwei; Mu, Feng; Yin, Ye; Yang, Huanming; Lisby, Michael; Cornall, Richard J; Mulder, Jan; Uhlén, Mathias; Esteban, Miguel A.; Li, Yuxiang; Liu, Longqi; Xu, Xun; Wang, Jian.

In: Cell, Vol. 185, No. 10, 2022, p. 1777-1792.e21.

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

Harvard

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, Q-F, Zhao, F, Chen, B, Li, M, Dai, X, Wang, S, Kuang, H, Hui, J, Wang, L, Fei, J-F, 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 2022, 'Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays', Cell, vol. 185, no. 10, pp. 1777-1792.e21. https://doi.org/10.1016/j.cell.2022.04.003

APA

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., ... Wang, J. (2022). Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell, 185(10), 1777-1792.e21. https://doi.org/10.1016/j.cell.2022.04.003

Vancouver

Chen A, Liao S, Cheng M, Ma K, Wu L, Lai Y et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell. 2022;185(10):1777-1792.e21. https://doi.org/10.1016/j.cell.2022.04.003

Author

Chen, Ao ; Liao, Sha ; Cheng, Mengnan ; Ma, Kailong ; Wu, Liang ; Lai, Yiwei ; Qiu, Xiaojie ; Yang, Jin ; Xu, Jiangshan ; Hao, Shijie ; Wang, Xin ; Lu, Huifang ; Chen, Xi ; Liu, Xing ; Huang, Xin ; Li, Zhao ; Hong, Yan ; Jiang, Yujia ; Peng, Jian ; Liu, Shuai ; Shen, Mengzhe ; Liu, Chuanyu ; Li, Quanshui ; Yuan, Yue ; Wei, Xiaoyu ; Zheng, Huiwen ; Feng, Weimin ; Wang, Zhifeng ; Liu, Yang ; Wang, Zhaohui ; Yang, Yunzhi ; Xiang, Haitao ; Han, Lei ; Qin, Baoming ; Guo, Pengcheng ; Lai, Guangyao ; Muñoz-Cánoves, Pura ; Maxwell, Patrick H ; Thiery, Jean Paul ; Wu, Qing-Feng ; Zhao, Fuxiang ; Chen, Bichao ; Li, Mei ; Dai, Xi ; Wang, Shuai ; Kuang, Haoyan ; Hui, Junhou ; Wang, Liqun ; Fei, Ji-Feng ; Wang, Ou ; Wei, Xiaofeng ; Lu, Haorong ; Wang, Bo ; Liu, Shiping ; Gu, Ying ; Ni, Ming ; Zhang, Wenwei ; Mu, Feng ; Yin, Ye ; Yang, Huanming ; Lisby, Michael ; Cornall, Richard J ; Mulder, Jan ; Uhlén, Mathias ; Esteban, Miguel A. ; Li, Yuxiang ; Liu, Longqi ; Xu, Xun ; Wang, Jian. / Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. In: Cell. 2022 ; Vol. 185, No. 10. pp. 1777-1792.e21.

Bibtex

@article{dd123904163c4267bf46c612c3bc3492,

title = "Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays",

abstract = "Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.",

keywords = "Animals, DNA/genetics, Embryo, Mammalian, Female, Gene Expression Profiling/methods, Mammals/genetics, Mice, Organogenesis/genetics, Pregnancy, Sequence Analysis, RNA/methods, Single-Cell Analysis/methods, Transcriptome/genetics",

author = "Ao Chen and Sha Liao and Mengnan Cheng and Kailong Ma and Liang Wu and Yiwei Lai and Xiaojie Qiu and Jin Yang and Jiangshan Xu and Shijie Hao and Xin Wang and Huifang Lu and Xi Chen and Xing Liu and Xin Huang and Zhao Li and Yan Hong and Yujia Jiang and Jian Peng and Shuai Liu and Mengzhe Shen and Chuanyu Liu and Quanshui Li and Yue Yuan and Xiaoyu Wei and Huiwen Zheng and Weimin Feng and Zhifeng Wang and Yang Liu and Zhaohui Wang and Yunzhi Yang and Haitao Xiang and Lei Han and Baoming Qin and Pengcheng Guo and Guangyao Lai and Pura Mu{\~n}oz-C{\'a}noves and Maxwell, {Patrick H} and Thiery, {Jean Paul} and Qing-Feng Wu and Fuxiang Zhao and Bichao Chen and Mei Li and Xi Dai and Shuai Wang and Haoyan Kuang and Junhou Hui and Liqun Wang and Ji-Feng Fei and Ou Wang and Xiaofeng Wei and Haorong Lu and Bo Wang and Shiping Liu and Ying Gu and Ming Ni and Wenwei Zhang and Feng Mu and Ye Yin and Huanming Yang and Michael Lisby and Cornall, {Richard J} and Jan Mulder and Mathias Uhl{\'e}n and Esteban, {Miguel A.} and Yuxiang Li and Longqi Liu and Xun Xu and Jian Wang",

year = "2022",

doi = "10.1016/j.cell.2022.04.003",

language = "English",

volume = "185",

pages = "1777--1792.e21",

journal = "Cell",

issn = "0092-8674",

publisher = "Cell Press",

number = "10",

}

RIS

TY - JOUR

T1 - Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

AU - Chen, Ao

AU - Liao, Sha

AU - Cheng, Mengnan

AU - Ma, Kailong

AU - Wu, Liang

AU - Lai, Yiwei

AU - Qiu, Xiaojie

AU - Yang, Jin

AU - Xu, Jiangshan

AU - Hao, Shijie

AU - Wang, Xin

AU - Lu, Huifang

AU - Chen, Xi

AU - Liu, Xing

AU - Huang, Xin

AU - Li, Zhao

AU - Hong, Yan

AU - Jiang, Yujia

AU - Peng, Jian

AU - Liu, Shuai

AU - Shen, Mengzhe

AU - Liu, Chuanyu

AU - Li, Quanshui

AU - Yuan, Yue

AU - Wei, Xiaoyu

AU - Zheng, Huiwen

AU - Feng, Weimin

AU - Wang, Zhifeng

AU - Liu, Yang

AU - Wang, Zhaohui

AU - Yang, Yunzhi

AU - Xiang, Haitao

AU - Han, Lei

AU - Qin, Baoming

AU - Guo, Pengcheng

AU - Lai, Guangyao

AU - Muñoz-Cánoves, Pura

AU - Maxwell, Patrick H

AU - Thiery, Jean Paul

AU - Wu, Qing-Feng

AU - Zhao, Fuxiang

AU - Chen, Bichao

AU - Li, Mei

AU - Dai, Xi

AU - Wang, Shuai

AU - Kuang, Haoyan

AU - Hui, Junhou

AU - Wang, Liqun

AU - Fei, Ji-Feng

AU - Wang, Ou

AU - Wei, Xiaofeng

AU - Lu, Haorong

AU - Wang, Bo

AU - Liu, Shiping

AU - Gu, Ying

AU - Ni, Ming

AU - Zhang, Wenwei

AU - Mu, Feng

AU - Yin, Ye

AU - Yang, Huanming

AU - Lisby, Michael

AU - Cornall, Richard J

AU - Mulder, Jan

AU - Uhlén, Mathias

AU - Esteban, Miguel A.

AU - Li, Yuxiang

AU - Liu, Longqi

AU - Xu, Xun

AU - Wang, Jian

PY - 2022

Y1 - 2022

N2 - Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.

AB - Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.

KW - Animals

KW - DNA/genetics

KW - Embryo, Mammalian

KW - Female

KW - Gene Expression Profiling/methods

KW - Mammals/genetics

KW - Mice

KW - Organogenesis/genetics

KW - Pregnancy

KW - Sequence Analysis, RNA/methods

KW - Single-Cell Analysis/methods

KW - Transcriptome/genetics

U2 - 10.1016/j.cell.2022.04.003

DO - 10.1016/j.cell.2022.04.003

M3 - Journal article

C2 - 35512705

VL - 185

SP - 1777-1792.e21

JO - Cell

JF - Cell

SN - 0092-8674

IS - 10

ER -

ID: 310380245

Department of Biology