Nature Methods最新文献

Multiplexing strategies to scale up brain organoid modeling.

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-18 DOI: 10.1038/s41592-024-02556-4

引用次数: 0

Considerations for building and using integrated single-cell atlases. 构建和使用集成单细胞图谱的注意事项。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-13 DOI: 10.1038/s41592-024-02532-y

Karin Hrovatin, Lisa Sikkema, Vladimir A Shitov, Graham Heimberg, Maiia Shulman, Amanda J Oliver, Michaela F Mueller, Ignacio L Ibarra, Hanchen Wang, Ciro Ramírez-Suástegui, Peng He, Anna C Schaar, Sarah A Teichmann, Fabian J Theis, Malte D Luecken

{"title":"Considerations for building and using integrated single-cell atlases.","authors":"Karin Hrovatin, Lisa Sikkema, Vladimir A Shitov, Graham Heimberg, Maiia Shulman, Amanda J Oliver, Michaela F Mueller, Ignacio L Ibarra, Hanchen Wang, Ciro Ramírez-Suástegui, Peng He, Anna C Schaar, Sarah A Teichmann, Fabian J Theis, Malte D Luecken","doi":"10.1038/s41592-024-02532-y","DOIUrl":"https://doi.org/10.1038/s41592-024-02532-y","url":null,"abstract":"The rapid adoption of single-cell technologies has created an opportunity to build single-cell 'atlases' integrating diverse datasets across many laboratories. Such atlases can serve as a reference for analyzing and interpreting current and future data. However, it has become apparent that atlasing approaches differ, and the impact of these differences are often unclear. Here we review the current atlasing literature and present considerations for building and using atlases. Importantly, we find that no one-size-fits-all protocol for atlas building exists, but rather we discuss context-specific considerations and workflows, including atlas conceptualization, data collection, curation and integration, atlas evaluation and atlas sharing. We further highlight the benefits of integrated atlases for analyses of new datasets and deriving biological insights beyond what is possible from individual datasets. Our overview of current practices and associated recommendations will improve the quality of atlases to come, facilitating the shift to a unified, reference-based understanding of single-cell biology.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

iFlpMosaics enable the multispectral barcoding and high-throughput comparative analysis of mutant and wild-type cells. iFlpMosaics 可对突变型和野生型细胞进行多光谱条形码和高通量比较分析。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-13 DOI: 10.1038/s41592-024-02534-w

Irene Garcia-Gonzalez, Stefano Gambera, Susana F Rocha, Alvaro Regano, Lourdes Garcia-Ortega, Mariya Lytvyn, Luis Diago-Domingo, Maria S Sanchez-Muñoz, Aroa Garcia-Cabero, Ivana Zagorac, Wen Luo, Macarena De Andrés-Laguillo, Macarena Fernández-Chacón, Verónica Casquero-Garcia, Federica Francesca Lunella, Carlos Torroja, Fátima Sánchez-Cabo, Rui Benedito

{"title":"iFlpMosaics enable the multispectral barcoding and high-throughput comparative analysis of mutant and wild-type cells.","authors":"Irene Garcia-Gonzalez, Stefano Gambera, Susana F Rocha, Alvaro Regano, Lourdes Garcia-Ortega, Mariya Lytvyn, Luis Diago-Domingo, Maria S Sanchez-Muñoz, Aroa Garcia-Cabero, Ivana Zagorac, Wen Luo, Macarena De Andrés-Laguillo, Macarena Fernández-Chacón, Verónica Casquero-Garcia, Federica Francesca Lunella, Carlos Torroja, Fátima Sánchez-Cabo, Rui Benedito","doi":"10.1038/s41592-024-02534-w","DOIUrl":"https://doi.org/10.1038/s41592-024-02534-w","url":null,"abstract":"To understand gene function, it is necessary to compare cells carrying the mutated target gene with normal cells. In most biomedical studies, the cells being compared are in different mutant and control animals and, therefore, do not experience the same epigenetic changes and tissue microenvironment. The experimental induction of genetic mosaics is essential to determine a gene cell-autonomous function and to model the etiology of diseases caused by somatic mutations. Current technologies used to induce genetic mosaics in mice lack either accuracy, throughput or barcoding diversity. Here we present the iFlpMosaics toolkit comprising a large set of new genetic tools and mouse lines that enable recombinase-dependent ratiometric induction and single-cell clonal tracking of multiple fluorescently labeled wild-type and Cre-mutant cells within the same time window and tissue microenvironment. The labeled cells can be profiled by multispectral imaging or by fluorescence-activated flow cytometry and single-cell RNA sequencing. iFlpMosaics facilitate the induction and analysis of genetic mosaics in any quiescent or progenitor cell, and for any given single or combination of floxed genes, thus enabling a more accurate understanding of how induced genetic mutations affect the biology of single cells during tissue development, homeostasis and disease.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Author Correction: Cell Painting: a decade of discovery and innovation in cellular imaging.

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-12 DOI: 10.1038/s41592-024-02578-y

Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E Carpenter

引用次数: 0

MouseGoggles: an immersive virtual reality headset for mouse neuroscience and behavior. MouseGoggles：用于小鼠神经科学和行为的沉浸式虚拟现实头戴设备。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-12 DOI: 10.1038/s41592-024-02540-y

Matthew Isaacson, Hongyu Chang, Laura Berkowitz, Rick Zirkel, Yusol Park, Danyu Hu, Ian Ellwood, Chris B Schaffer

引用次数: 0

Moculus: an immersive virtual reality system for mice incorporating stereo vision. Moculus：结合立体视觉的小鼠沉浸式虚拟现实系统。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-12 DOI: 10.1038/s41592-024-02554-6

Linda Judák, Gergely Dobos, Katalin Ócsai, Eszter Báthory, Huba Szebik, Balázs Tarján, Pál Maák, Zoltán Szadai, István Takács, Balázs Chiovini, Tibor Lőrincz, Áron Szepesi, Botond Roska, Gergely Szalay, Balázs Rózsa

{"title":"Moculus: an immersive virtual reality system for mice incorporating stereo vision.","authors":"Linda Judák, Gergely Dobos, Katalin Ócsai, Eszter Báthory, Huba Szebik, Balázs Tarján, Pál Maák, Zoltán Szadai, István Takács, Balázs Chiovini, Tibor Lőrincz, Áron Szepesi, Botond Roska, Gergely Szalay, Balázs Rózsa","doi":"10.1038/s41592-024-02554-6","DOIUrl":"https://doi.org/10.1038/s41592-024-02554-6","url":null,"abstract":"Due to technical roadblocks, it is unclear how visual circuits represent multiple features or how behaviorally relevant representations are selected for long-term memory. Here we developed Moculus, a head-mounted virtual reality platform for mice that covers the entire visual field, and allows binocular depth perception and full visual immersion. This controllable environment, with three-dimensional (3D) corridors and 3D objects, in combination with 3D acousto-optical imaging, affords rapid visual learning and the uncovering of circuit substrates in one measurement session. Both the control and reinforcement-associated visual cue coding neuronal assemblies are transiently expanded by reinforcement feedback to near-saturation levels. This increases computational capability and allows competition among assemblies that encode behaviorally relevant information. The coding assemblies form partially orthogonal and overlapping clusters centered around hub cells with higher and earlier ramp-like responses, as well as locally increased functional connectivity.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-molecule DNA dynamics with graphene energy transfer.

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-10 DOI: 10.1038/s41592-024-02560-8

Pallav Kosuri

引用次数: 0

A peptide-centric local stability assay enables proteome-scale identification of the protein targets and binding regions of diverse ligands.

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-10 DOI: 10.1038/s41592-024-02553-7

Kejia Li, Shijie Chen, Keyun Wang, Yan Wang, Lianji Xue, Yuying Ye, Zheng Fang, Jiawen Lyu, Haiyang Zhu, Yanan Li, Ting Yu, Feng Yang, Xiaolei Zhang, Siqi Guo, Chengfei Ruan, Jiahua Zhou, Qi Wang, Mingming Dong, Cheng Luo, Mingliang Ye

引用次数: 0

ProHap enables human proteomic database generation accounting for population diversity.

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-09 DOI: 10.1038/s41592-024-02506-0

Jakub Vašíček, Ksenia G Kuznetsova, Dafni Skiadopoulou, Lucas Unger, Simona Chera, Luiza M Ghila, Nuno Bandeira, Pål R Njølstad, Stefan Johansson, Stefan Bruckner, Lukas Käll, Marc Vaudel

引用次数: 0

Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution.

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-12-09 DOI: 10.1038/s41592-024-02555-5

Nicolò Caporale, Davide Castaldi, Marco Tullio Rigoli, Cristina Cheroni, Alessia Valenti, Sarah Stucchi, Manuel Lessi, Davide Bulgheresi, Sebastiano Trattaro, Martina Pezzali, Alessandro Vitriolo, Alejandro Lopez-Tobon, Matteo Bonfanti, Dario Ricca, Katharina T Schmid, Matthias Heinig, Fabian J Theis, Carlo Emanuele Villa, Giuseppe Testa

{"title":"Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution.","authors":"Nicolò Caporale, Davide Castaldi, Marco Tullio Rigoli, Cristina Cheroni, Alessia Valenti, Sarah Stucchi, Manuel Lessi, Davide Bulgheresi, Sebastiano Trattaro, Martina Pezzali, Alessandro Vitriolo, Alejandro Lopez-Tobon, Matteo Bonfanti, Dario Ricca, Katharina T Schmid, Matthias Heinig, Fabian J Theis, Carlo Emanuele Villa, Giuseppe Testa","doi":"10.1038/s41592-024-02555-5","DOIUrl":"10.1038/s41592-024-02555-5","url":null,"abstract":"Dissecting human neurobiology at high resolution and with mechanistic precision requires a major leap in scalability, given the need for experimental designs that include multiple individuals and, prospectively, population cohorts. To lay the foundation for this, we have developed and benchmarked complementary strategies to multiplex brain organoids by pooling cells from different pluripotent stem cell (PSC) lines either during organoid generation (mosaic models) or before single-cell RNA sequencing (scRNA-seq) library preparation (downstream multiplexing). We have also developed a new computational method, SCanSNP, and a consensus call to deconvolve cell identities, overcoming current criticalities in doublets and low-quality cell identification. We validated both multiplexing methods for charting neurodevelopmental trajectories at high resolution, thus linking specific individuals' trajectories to genetic variation. Finally, we modeled their scalability across different multiplexing combinations and showed that mosaic organoids represent an enabling method for high-throughput settings. Together, this multiplexing suite of experimental and computational methods provides a highly scalable resource for brain disease and neurodiversity modeling.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0