Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pbio.3002912
Download full text from publisher
References listed on IDEAS
- Aparna Bhaduri & Carmen Sandoval-Espinosa & Marcos Otero-Garcia & Irene Oh & Raymund Yin & Ugomma C. Eze & Tomasz J. Nowakowski & Arnold R. Kriegstein, 2021. "An atlas of cortical arealization identifies dynamic molecular signatures," Nature, Nature, vol. 598(7879), pages 200-204, October.
- Alessandro Fiorenzano & Edoardo Sozzi & Marcella Birtele & Janko Kajtez & Jessica Giacomoni & Fredrik Nilsson & Andreas Bruzelius & Yogita Sharma & Yu Zhang & Bengt Mattsson & Jenny Emnéus & Daniella , 2021. "Single-cell transcriptomics captures features of human midbrain development and dopamine neuron diversity in brain organoids," Nature Communications, Nature, vol. 12(1), pages 1-19, December.
- Toshiro Sato & Robert G. Vries & Hugo J. Snippert & Marc van de Wetering & Nick Barker & Daniel E. Stange & Johan H. van Es & Arie Abo & Pekka Kujala & Peter J. Peters & Hans Clevers, 2009. "Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche," Nature, Nature, vol. 459(7244), pages 262-265, May.
- Giorgia Quadrato & Tuan Nguyen & Evan Z. Macosko & John L. Sherwood & Sung Min Yang & Daniel R. Berger & Natalie Maria & Jorg Scholvin & Melissa Goldman & Justin P. Kinney & Edward S. Boyden & Jeff W., 2017. "Cell diversity and network dynamics in photosensitive human brain organoids," Nature, Nature, vol. 545(7652), pages 48-53, May.
- Sergiu P. Pașca & Paola Arlotta & Helen S. Bateup & J. Gray Camp & Silvia Cappello & Fred H. Gage & Jürgen A. Knoblich & Arnold R. Kriegstein & Madeline A. Lancaster & Guo-Li Ming & Alysson R. Muotri , 2022. "A nomenclature consensus for nervous system organoids and assembloids," Nature, Nature, vol. 609(7929), pages 907-910, September.
- Omer Revah & Felicity Gore & Kevin W. Kelley & Jimena Andersen & Noriaki Sakai & Xiaoyu Chen & Min-Yin Li & Fikri Birey & Xiao Yang & Nay L. Saw & Samuel W. Baker & Neal D. Amin & Shravanti Kulkarni &, 2022. "Maturation and circuit integration of transplanted human cortical organoids," Nature, Nature, vol. 610(7931), pages 319-326, October.
- Zhisong He & Leander Dony & Jonas Simon Fleck & Artur Szałata & Katelyn X. Li & Irena Slišković & Hsiu-Chuan Lin & Malgorzata Santel & Alexander Atamian & Giorgia Quadrato & Jieran Sun & Sergiu P. Paș, 2024. "An integrated transcriptomic cell atlas of human neural organoids," Nature, Nature, vol. 635(8039), pages 690-698, November.
- Fikri Birey & Jimena Andersen & Christopher D. Makinson & Saiful Islam & Wu Wei & Nina Huber & H. Christina Fan & Kimberly R. Cordes Metzler & Georgia Panagiotakos & Nicholas Thom & Nancy A. O’Rourke , 2017. "Assembly of functionally integrated human forebrain spheroids," Nature, Nature, vol. 545(7652), pages 54-59, May.
- Sabina Kanton & Michael James Boyle & Zhisong He & Malgorzata Santel & Anne Weigert & Fátima Sanchís-Calleja & Patricia Guijarro & Leila Sidow & Jonas Simon Fleck & Dingding Han & Zhengzong Qian & Mic, 2019. "Organoid single-cell genomic atlas uncovers human-specific features of brain development," Nature, Nature, vol. 574(7778), pages 418-422, October.
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.- Anna Pagliaro & Roxy Finger & Iris Zoutendijk & Saskia Bunschuh & Hans Clevers & Delilah Hendriks & Benedetta Artegiani, 2023. "Temporal morphogen gradient-driven neural induction shapes single expanded neuroepithelium brain organoids with enhanced cortical identity," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Maisumu Gulimiheranmu & Shuang Li & Junmei Zhou, 2021. "In Vitro Recapitulation of Neuropsychiatric Disorders with Pluripotent Stem Cells-Derived Brain Organoids," IJERPH, MDPI, vol. 18(23), pages 1-14, November.
- Anand Ramani & Giovanni Pasquini & Niklas J. Gerkau & Vaibhav Jadhav & Omkar Suhas Vinchure & Nazlican Altinisik & Hannes Windoffer & Sarah Muller & Ina Rothenaigner & Sean Lin & Aruljothi Mariappan &, 2024. "Reliability of high-quantity human brain organoids for modeling microcephaly, glioma invasion and drug screening," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
- Elaine T. Lim & Yingleong Chan & Pepper Dawes & Xiaoge Guo & Serkan Erdin & Derek J. C. Tai & Songlei Liu & Julia M. Reichert & Mannix J. Burns & Ying Kai Chan & Jessica J. Chiang & Katharina Meyer & , 2022. "Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
- Tal Sharf & Tjitse Molen & Stella M. K. Glasauer & Elmer Guzman & Alessio P. Buccino & Gabriel Luna & Zhuowei Cheng & Morgane Audouard & Kamalini G. Ranasinghe & Kiwamu Kudo & Srikantan S. Nagarajan &, 2022. "Functional neuronal circuitry and oscillatory dynamics in human brain organoids," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
- Yueqi Wang & Simone Chiola & Guang Yang & Chad Russell & Celeste J. Armstrong & Yuanyuan Wu & Jay Spampanato & Paisley Tarboton & H. M. Arif Ullah & Nicolas U. Edgar & Amelia N. Chang & David A. Harmi, 2022. "Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes," Nature Communications, Nature, vol. 13(1), pages 1-25, December.
- Rebecca Sebastian & Kang Jin & Narciso Pavon & Ruby Bansal & Andrew Potter & Yoonjae Song & Juliana Babu & Rafael Gabriel & Yubing Sun & Bruce Aronow & ChangHui Pak, 2023. "Schizophrenia-associated NRXN1 deletions induce developmental-timing- and cell-type-specific vulnerabilities in human brain organoids," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Xiangling Feng & Yingjie Gao & Fan Chu & Yuwen Shan & Meicheng Liu & Yaoyi Wang & Ying Zhu & Qing Lu & Mingfeng Li, 2025. "Cortical arealization of interneurons defines shared and distinct molecular programs in developing human and macaque brains," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
- Pushkal Sharma & Colin Y. Kim & Heather R. Keys & Shinya Imada & Alex B. Joseph & Luke Ferro & Tenzin Kunchok & Rachel Anderson & Yulin Sun & Ömer H. Yilmaz & Jing-Ke Weng & Ankur Jain, 2025. "Genetically encoded fluorescent reporter for polyamines," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
- Xuelong Yao & Zongyang Lu & Zhanying Feng & Lei Gao & Xin Zhou & Min Li & Suijuan Zhong & Qian Wu & Zhenbo Liu & Haofeng Zhang & Zeyuan Liu & Lizhi Yi & Tao Zhou & Xudong Zhao & Jun Zhang & Yong Wang , 2022. "Comparison of chromatin accessibility landscapes during early development of prefrontal cortex between rhesus macaque and human," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Chang Liu & Xiaojiao Zheng & Jian Ji & Xuan Zhu & Xiaoning Liu & He Liu & Lichun Guo & Kun Ye & Shuang Zhang & Yong-jiang Xu & Xiulan Sun & Weibiao Zhou & Hoi Leong Xavier Wong & Yaoqi Tian & He Qian, 2025. "The carotenoid torularhodin alleviates NAFLD by promoting Akkermanisa muniniphila-mediated adenosylcobalamin metabolism," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
- Francesco Matteo & Rebecca Bonrath & Veronica Pravata & Hanna Schmidt & Ane Cristina Ayo Martin & Rossella Giaimo & Danusa Menegaz & Stephan Riesenberg & Femke M. S. Vrij & Giuseppina Maccarrone & Mar, 2025. "Neuronal hyperactivity in neurons derived from individuals with gray matter heterotopia," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
- Antonella Fazio & Dora Bordoni & Jan W. P. Kuiper & Saskia Weber-Stiehl & Stephanie T. Stengel & Philipp Arnold & David Ellinghaus & Go Ito & Florian Tran & Berith Messner & Anna Henning & Joana P. Be, 2022. "DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
- Enara Larrañaga & Miquel Marin-Riera & Aina Abad-Lázaro & David Bartolomé-Català & Aitor Otero & Vanesa Fernández-Majada & Eduard Batlle & James Sharpe & Samuel Ojosnegros & Jordi Comelles & Elena Mar, 2025. "Long-range organization of intestinal 2D-crypts using exogenous Wnt3a micropatterning," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
- Tsunaki Higa & Yasutaka Okita & Akinobu Matsumoto & Shogo Nakayama & Takeru Oka & Osamu Sugahara & Daisuke Koga & Shoichiro Takeishi & Hirokazu Nakatsumi & Naoki Hosen & Sylvie Robine & Makoto M. Take, 2022. "Spatiotemporal reprogramming of differentiated cells underlies regeneration and neoplasia in the intestinal epithelium," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
- Suran Kim & Sungjin Min & Yi Sun Choi & Sung-Hyun Jo & Jae Hun Jung & Kyusun Han & Jin Kim & Soohwan An & Yong Woo Ji & Yun-Gon Kim & Seung-Woo Cho, 2022. "Tissue extracellular matrix hydrogels as alternatives to Matrigel for culturing gastrointestinal organoids," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
- Tatsuya Osaki & Tomoya Duenki & Siu Yu A. Chow & Yasuhiro Ikegami & Romain Beaubois & Timothée Levi & Nao Nakagawa-Tamagawa & Yoji Hirano & Yoshiho Ikeuchi, 2024. "Complex activity and short-term plasticity of human cerebral organoids reciprocally connected with axons," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Jia-Ru Wei & Zhao-Zhe Hao & Chuan Xu & Mengyao Huang & Lei Tang & Nana Xu & Ruifeng Liu & Yuhui Shen & Sarah A. Teichmann & Zhichao Miao & Sheng Liu, 2022. "Identification of visual cortex cell types and species differences using single-cell RNA sequencing," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
- Allen W. Lynch & Myles Brown & Clifford A. Meyer, 2023. "Multi-batch single-cell comparative atlas construction by deep learning disentanglement," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
- Clara Morral & Arshad Ayyaz & Hsuan-Cheng Kuo & Mardi Fink & Ioannis I. Verginadis & Andrea R. Daniel & Danielle N. Burner & Lucy M. Driver & Sloane Satow & Stephanie Hasapis & Reem Ghinnagow & Lixia , 2024. "p53 promotes revival stem cells in the regenerating intestine after severe radiation injury," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
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:plo:pbio00:3002912. 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: plosbiology (email available below). General contact details of provider: https://journals.plos.org/plosbiology/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.