Data licenses
Here follows a list of references to the data used, alongside with the respective citation, link to the data, link and information of the license.
| Data | Citation | Download link | Is derived | License link | License information (as of 12.12.2023) |
|---|---|---|---|---|---|
| Allen Brain Atlas Mouse Brain Template & Parcellation | Allen Reference Atlas – Adult Mouse. Available from atlas.brain-map.org. Quanxin Wang, Song-Lin Ding, Yang Li, Josh Royall, David Feng, Phil Lesnar, Nile Graddis, Maitham Naeemi, Benjamin Facer, Anh Ho, Tim Dolbeare, Brandon Blanchard, Nick Dee, Wayne Wakeman, Karla E. Hirokawa, Aaron Szafer, Susan M. Sunkin, Seung Wook Oh, Amy Bernard, John W. Phillips, Michael Hawrylycz, Christof Koch, Hongkui Zeng, Julie A. Harris, Lydia Ng, The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas, Cell, Volume 181, Issue 4, 2020 | http://help.brain-map.org/display/mouseconnectivity/API#API-DownloadAtlas3-DReferenceModels | Original data | https://alleninstitute.org/legal/terms-use/ | "You may use, copy, distribute, publicly perform, publicly display, or create derivative works of the Content (except our name, trademarks, or logos pursuant to the Trademarks section below) for research or other noncommercial purposes. Any derivative works (defined as “Improvements” below) are subject to the “Freedom to Innovate and Rights to Improvements” section of these Terms. In addition, where the Content contains links to downloadable software applications, services, or tools, you may download and use such applications, services, or tools as long as you adhere to any license terms and conditions provided with those applications, services, or tools. You may not redistribute the Content or Improvements for commercial purposes without our written permission. For purposes of these Terms, commercial purposes is the incorporation of the Allen Institute's Content into anything that is designed for the purpose of sale or use of the Content to perform a commercial service for a third party; however, because we encourage use of our Content for research and academic publication, you may, without obtaining further license or permission, publish a limited set of the Content in a scholarly journal, textbook or other professional, academic or journalistic publication (with appropriate citation) and still be compliant with these Terms. To request permission for commercial purposes, please email terms@alleninstitute.org." |
| Allen Brain Atlas Connectivity Data | Axonal projections of 2173 injections sites labeled by rAAV tracers and visualized using serial two-photon tomography (connectivity.brain-map.org). Data has been mirrored to be available on both hemispheres, resulting in a total of 4346 injection sites. Oh, S. W., Harris, J. A., Ng, L., Winslow, B., Cain, N., Mihalas, S., Wang, Q., Lau, C., Kuan, L., Henry, A. M., Mortrud, M. T., Ouellette, B., Nguyen, T. N., Sorensen, S. A., Slaughterbeck, C. R., Wakeman, W., Li, Y., Feng, D., Ho, A., Nicholas, E., … Zeng, H. (2014). A mesoscale connectome of the mouse brain. Nature, 508(7495), 207–214. https://doi.org/10.1038/nature13186 | API - Mouse Connectivity (brain-map.org) | Original data | https://alleninstitute.org/legal/terms-use/ | "You may use, copy, distribute, publicly perform, publicly display, or create derivative works of the Content (except our name, trademarks, or logos pursuant to the Trademarks section below) for research or other noncommercial purposes. Any derivative works (defined as “Improvements” below) are subject to the “Freedom to Innovate and Rights to Improvements” section of these Terms. In addition, where the Content contains links to downloadable software applications, services, or tools, you may download and use such applications, services, or tools as long as you adhere to any license terms and conditions provided with those applications, services, or tools. You may not redistribute the Content or Improvements for commercial purposes without our written permission. For purposes of these Terms, commercial purposes is the incorporation of the Allen Institute's Content into anything that is designed for the purpose of sale or use of the Content to perform a commercial service for a third party; however, because we encourage use of our Content for research and academic publication, you may, without obtaining further license or permission, publish a limited set of the Content in a scholarly journal, textbook or other professional, academic or journalistic publication (with appropriate citation) and still be compliant with these Terms. To request permission for commercial purposes, please email terms@alleninstitute.org." |
| Allen Brain Atlas Human Brain Parcellation | © 2019 Allen Institute for Brain Science. Song‐Lin Ding, Joshua J. Royall, Susan M. Sunkin, Benjamin A.C. Facer, Phil Lesnar, Amy Bernard, Lydia Ng, Ed S. Lein (2020). Allen Human Reference Atlas – 3D, 2020 RRID:SCR_017764, version 1.0.0. | http://download.alleninstitute.org/informatics-archive/allen_human_reference_atlas_3d_2020/version_1 | Original data | https://alleninstitute.org/legal/terms-use/ | "You may use, copy, distribute, publicly perform, publicly display, or create derivative works of the Content (except our name, trademarks, or logos pursuant to the Trademarks section below) for research or other noncommercial purposes. Any derivative works (defined as “Improvements” below) are subject to the “Freedom to Innovate and Rights to Improvements” section of these Terms. In addition, where the Content contains links to downloadable software applications, services, or tools, you may download and use such applications, services, or tools as long as you adhere to any license terms and conditions provided with those applications, services, or tools. You may not redistribute the Content or Improvements for commercial purposes without our written permission. For purposes of these Terms, commercial purposes is the incorporation of the Allen Institute's Content into anything that is designed for the purpose of sale or use of the Content to perform a commercial service for a third party; however, because we encourage use of our Content for research and academic publication, you may, without obtaining further license or permission, publish a limited set of the Content in a scholarly journal, textbook or other professional, academic or journalistic publication (with appropriate citation) and still be compliant with these Terms. To request permission for commercial purposes, please email terms@alleninstitute.org." |
| Lein_2007 | Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A. F., Boguski, M. S., Brockway, K. S., Byrnes, E. J., Chen, L., Chen, L., Chen, T. M., Chin, M. C., Chong, J., Crook, B. E., Czaplinska, A., Dang, C. N., Datta, S., Dee, N. R., … Jones, A. R. (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445(7124), 168–176. | http://help.brain-map.org/display/mousebrain/API | Original data | https://alleninstitute.org/legal/terms-use/ | "You may use, copy, distribute, publicly perform, publicly display, or create derivative works of the Content (except our name, trademarks, or logos pursuant to the Trademarks section below) for research or other noncommercial purposes. Any derivative works (defined as “Improvements” below) are subject to the “Freedom to Innovate and Rights to Improvements” section of these Terms. In addition, where the Content contains links to downloadable software applications, services, or tools, you may download and use such applications, services, or tools as long as you adhere to any license terms and conditions provided with those applications, services, or tools. You may not redistribute the Content or Improvements for commercial purposes without our written permission. For purposes of these Terms, commercial purposes is the incorporation of the Allen Institute's Content into anything that is designed for the purpose of sale or use of the Content to perform a commercial service for a third party; however, because we encourage use of our Content for research and academic publication, you may, without obtaining further license or permission, publish a limited set of the Content in a scholarly journal, textbook or other professional, academic or journalistic publication (with appropriate citation) and still be compliant with these Terms. To request permission for commercial purposes, please email terms@alleninstitute.org." |
| Hawrylycz_2012 | Hawrylycz, M. J., Lein, E. S., Guillozet-Bongaarts, A. L., Shen, E. H., Ng, L., Miller, J. A., van de Lagemaat, L. N., Smith, K. A., Ebbert, A., Riley, Z. L., Abajian, C., Beckmann, C. F., Bernard, A., Bertagnolli, D., Boe, A. F., Cartagena, P. M., Chakravarty, M. M., Chapin, M., Chong, J., Dalley, R. A., … Jones, A. R. (2012). An anatomically comprehensive atlas of the adult human brain transcriptome. Nature, 489(7416), 391–399. | https://portal.brain-map.org/atlases-and-data/rnaseq | Data is aggregated on sample/cell level. Original data can under no circumnstances be retrieved from BrainTrawler | https://alleninstitute.org/legal/terms-use/ | "You may use, copy, distribute, publicly perform, publicly display, or create derivative works of the Content (except our name, trademarks, or logos pursuant to the Trademarks section below) for research or other noncommercial purposes. Any derivative works (defined as “Improvements” below) are subject to the “Freedom to Innovate and Rights to Improvements” section of these Terms. In addition, where the Content contains links to downloadable software applications, services, or tools, you may download and use such applications, services, or tools as long as you adhere to any license terms and conditions provided with those applications, services, or tools. You may not redistribute the Content or Improvements for commercial purposes without our written permission. For purposes of these Terms, commercial purposes is the incorporation of the Allen Institute's Content into anything that is designed for the purpose of sale or use of the Content to perform a commercial service for a third party; however, because we encourage use of our Content for research and academic publication, you may, without obtaining further license or permission, publish a limited set of the Content in a scholarly journal, textbook or other professional, academic or journalistic publication (with appropriate citation) and still be compliant with these Terms. To request permission for commercial purposes, please email terms@alleninstitute.org." |
| Yao_2021 | Yao, Z., van Velthoven, C., Nguyen, T. N., Goldy, J., Sedeno-Cortes, A. E., Baftizadeh, F., Bertagnolli, D., Casper, T., Chiang, M., Crichton, K., Ding, S. L., Fong, O., Garren, E., Glandon, A., Gouwens, N. W., Gray, J., Graybuck, L. T., Hawrylycz, M. J., Hirschstein, D., Kroll, M., … Zeng, H. (2021). A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. Cell, 184(12), 3222–3241.e26. | https://portal.brain-map.org/atlases-and-data/rnaseq | Data is aggregated on sample/cell level. Original data can under no circumnstances be retrieved from BrainTrawler | https://alleninstitute.org/legal/terms-use/ | "You may use, copy, distribute, publicly perform, publicly display, or create derivative works of the Content (except our name, trademarks, or logos pursuant to the Trademarks section below) for research or other noncommercial purposes. Any derivative works (defined as “Improvements” below) are subject to the “Freedom to Innovate and Rights to Improvements” section of these Terms. In addition, where the Content contains links to downloadable software applications, services, or tools, you may download and use such applications, services, or tools as long as you adhere to any license terms and conditions provided with those applications, services, or tools. You may not redistribute the Content or Improvements for commercial purposes without our written permission. For purposes of these Terms, commercial purposes is the incorporation of the Allen Institute's Content into anything that is designed for the purpose of sale or use of the Content to perform a commercial service for a third party; however, because we encourage use of our Content for research and academic publication, you may, without obtaining further license or permission, publish a limited set of the Content in a scholarly journal, textbook or other professional, academic or journalistic publication (with appropriate citation) and still be compliant with these Terms. To request permission for commercial purposes, please email terms@alleninstitute.org." |
| Gouwens_2020 | Gouwens, N. W., Sorensen, S. A., Baftizadeh, F., Budzillo, A., Lee, B. R., Jarsky, T., Alfiler, L., Baker, K., Barkan, E., Berry, K., Bertagnolli, D., Bickley, K., Bomben, J., Braun, T., Brouner, K., Casper, T., Crichton, K., Daigle, T. L., Dalley, R., de Frates, R. A., … Zeng, H. (2020). Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells. Cell, 183(4), 935–953.e19. | https://portal.brain-map.org/atlases-and-data/rnaseq | Data is aggregated on sample/cell level. Original data can under no circumnstances be retrieved from BrainTrawler | https://alleninstitute.org/legal/terms-use/ | "You may use, copy, distribute, publicly perform, publicly display, or create derivative works of the Content (except our name, trademarks, or logos pursuant to the Trademarks section below) for research or other noncommercial purposes. Any derivative works (defined as “Improvements” below) are subject to the “Freedom to Innovate and Rights to Improvements” section of these Terms. In addition, where the Content contains links to downloadable software applications, services, or tools, you may download and use such applications, services, or tools as long as you adhere to any license terms and conditions provided with those applications, services, or tools. You may not redistribute the Content or Improvements for commercial purposes without our written permission. For purposes of these Terms, commercial purposes is the incorporation of the Allen Institute's Content into anything that is designed for the purpose of sale or use of the Content to perform a commercial service for a third party; however, because we encourage use of our Content for research and academic publication, you may, without obtaining further license or permission, publish a limited set of the Content in a scholarly journal, textbook or other professional, academic or journalistic publication (with appropriate citation) and still be compliant with these Terms. To request permission for commercial purposes, please email terms@alleninstitute.org." |
| Hodge_2019 | Hodge, R. D., Bakken, T. E., Miller, J. A., Smith, K. A., Barkan, E. R., Graybuck, L. T., Close, J. L., Long, B., Johansen, N., Penn, O., Yao, Z., Eggermont, J., Höllt, T., Levi, B. P., Shehata, S. I., Aevermann, B., Beller, A., Bertagnolli, D., Brouner, K., Casper, T., … Lein, E. S. (2019). Conserved cell types with divergent features in human versus mouse cortex. Nature, 573(7772), 61–68. | https://portal.brain-map.org/atlases-and-data/rnaseq | Data is aggregated on sample/cell level. Original data can under no circumnstances be retrieved from BrainTrawler | https://alleninstitute.org/legal/terms-use/ | "You may use, copy, distribute, publicly perform, publicly display, or create derivative works of the Content (except our name, trademarks, or logos pursuant to the Trademarks section below) for research or other noncommercial purposes. Any derivative works (defined as “Improvements” below) are subject to the “Freedom to Innovate and Rights to Improvements” section of these Terms. In addition, where the Content contains links to downloadable software applications, services, or tools, you may download and use such applications, services, or tools as long as you adhere to any license terms and conditions provided with those applications, services, or tools. You may not redistribute the Content or Improvements for commercial purposes without our written permission. For purposes of these Terms, commercial purposes is the incorporation of the Allen Institute's Content into anything that is designed for the purpose of sale or use of the Content to perform a commercial service for a third party; however, because we encourage use of our Content for research and academic publication, you may, without obtaining further license or permission, publish a limited set of the Content in a scholarly journal, textbook or other professional, academic or journalistic publication (with appropriate citation) and still be compliant with these Terms. To request permission for commercial purposes, please email terms@alleninstitute.org." |
| BrainSpan_2013 | BrainSpan Atlas of the Developing Human Brain. Funded by ARRA Awards 1RC2MH089921-01, 1RC2MH090047-01, and 1RC2MH089929-01. ©2011. Available from: http://brainspan.org. | https://portal.brain-map.org/atlases-and-data/rnaseq | Data is aggregated on sample/cell level. Original data can under no circumnstances be retrieved from BrainTrawler | https://alleninstitute.org/legal/terms-use/ | "You may use, copy, distribute, publicly perform, publicly display, or create derivative works of the Content (except our name, trademarks, or logos pursuant to the Trademarks section below) for research or other noncommercial purposes. Any derivative works (defined as “Improvements” below) are subject to the “Freedom to Innovate and Rights to Improvements” section of these Terms. In addition, where the Content contains links to downloadable software applications, services, or tools, you may download and use such applications, services, or tools as long as you adhere to any license terms and conditions provided with those applications, services, or tools. You may not redistribute the Content or Improvements for commercial purposes without our written permission. For purposes of these Terms, commercial purposes is the incorporation of the Allen Institute's Content into anything that is designed for the purpose of sale or use of the Content to perform a commercial service for a third party; however, because we encourage use of our Content for research and academic publication, you may, without obtaining further license or permission, publish a limited set of the Content in a scholarly journal, textbook or other professional, academic or journalistic publication (with appropriate citation) and still be compliant with these Terms. To request permission for commercial purposes, please email terms@alleninstitute.org." |
| Human Template (152 MNI) | Copyright (C) 1993–2009 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University | https://nist.mni.mcgill.ca/mni-icbm152-non-linear-6th-generation-symmetric-average-brain-stereotaxic-registration-model/ | Original data | https://nist.mni.mcgill.ca/mni-icbm152-non-linear-6th-generation-symmetric-average-brain-stereotaxic-registration-model/ | Copyright (C) 1993–2009 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University. Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies. The authors and McGill University make no representations about the suitability of this software for any purpose. It is provided “as is” without express or implied warranty. The authors are not responsible for any data loss, equipment damage, property loss, or injury to subjects or patients resulting from the use or misuse of this software package. |
| HumanConnectome Project DB | Resting-state connectivity (WU-Minn HCP Data db.humanconnectome.org). Van Essen, D. C., Smith, S. M., Barch, D. M., Behrens, T. E., Yacoub, E., Ugurbil, K., & WU-Minn HCP Consortium (2013). The WU-Minn Human Connectome Project: an overview. NeuroImage, 80, 62–79. | db.humanconnectome.org | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.humanconnectome.org/study/hcp-young-adult/document/wu-minn-hcp-consortium-open-access-data-use-terms | Data were provided [in part] by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657) funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University. |
| Gokce_2016 | Gokce, O., Stanley, G. M., Treutlein, B., Neff, N. F., Camp, J. G., Malenka, R. C., Rothwell, P. E., Fuccillo, M. V., Südhof, T. C., & Quake, S. R. (2016). Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq. Cell reports, 16(4), 1126–1137. | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE82187 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Bhattacherjee_2019 | Bhattacherjee, A., Djekidel, M. N., Chen, R., Chen, W., Tuesta, L. M., & Zhang, Y. (2019). Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction. Nature communications, 10(1), 4169. | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124952 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Campbell_2017 | Campbell, J. N., Macosko, E. Z., Fenselau, H., Pers, T. H., Lyubetskaya, A., Tenen, D., Goldman, M., Verstegen, A. M., Resch, J. M., McCarroll, S. A., Rosen, E. D., Lowell, B. B., & Tsai, L. T. (2017). A molecular census of arcuate hypothalamus and median eminence cell types. Nature neuroscience, 20(3), 484–496. | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90806 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Rossi_2019 | Rossi, M. A., Basiri, M. L., McHenry, J. A., Kosyk, O., Otis, J. M., van den Munkhof, H. E., Bryois, J., Hübel, C., Breen, G., Guo, W., Bulik, C. M., Sullivan, P. F., & Stuber, G. D. (2019). Obesity remodels activity and transcriptional state of a lateral hypothalamic brake on feeding. Science (New York, N.Y.), 364(6447), 1271–1274. | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE130597 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Lee_2020 | Lee, H., Fenster, R. J., Pineda, S. S., Gibbs, W. S., Mohammadi, S., Davila-Velderrain, J., Garcia, F. J., Therrien, M., Novis, H. S., Gao, F., Wilkinson, H., Vogt, T., Kellis, M., LaVoie, M. J., & Heiman, M. (2020). Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation. Neuron, 107(5), 891–908.e8. | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152058 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Song_2020_Darmanis_2015 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Darmanis, S., Sloan, S. A., Zhang, Y., Enge, M., Caneda, C., Shuer, L. M., Hayden Gephart, M. G., Barres, B. A., & Quake, S. R. (2015). A survey of human brain transcriptome diversity at the single cell level. Proceedings of the National Academy of Sciences of the United States of America, 112(23), 7285–7290. | https://mai.fudan.edu.cn/stab/help/ original: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67835 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Song_2020_Zhong_2018 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Zhong, S., Zhang, S., Fan, X., Wu, Q., Yan, L., Dong, J., Zhang, H., Li, L., Sun, L., Pan, N., Xu, X., Tang, F., Zhang, J., Qiao, J., & Wang, X. (2018). A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature, 555(7697), 524–528. | https://mai.fudan.edu.cn/stab/help/ original: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104276 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Song_2020_Fan_2018 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Fan, X., Dong, J., Zhong, S., Wei, Y., Wu, Q., Yan, L., Yong, J., Sun, L., Wang, X., Zhao, Y., Wang, W., Yan, J., Wang, X., Qiao, J., & Tang, F. (2018). Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis. Cell research, 28(7), 730–745. | https://mai.fudan.edu.cn/stab/help/ original: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103723 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Song_2020_Lake_2018 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Lake, B. B., Chen, S., Sos, B. C., Fan, J., Kaeser, G. E., Yung, Y. C., Duong, T. E., Gao, D., Chun, J., Kharchenko, P. V., & Zhang, K. (2018). Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nature biotechnology, 36(1), 70–80. | https://mai.fudan.edu.cn/stab/help/ original: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97942 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Song_2020_La_Manno_2016 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and La Manno, G., Gyllborg, D., Codeluppi, S., Nishimura, K., Salto, C., Zeisel, A., Borm, L. E., Stott, S., Toledo, E. M., Villaescusa, J. C., Lönnerberg, P., Ryge, J., Barker, R. A., Arenas, E., & Linnarsson, S. (2016). Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. Cell, 167(2), 566–580.e19. | https://mai.fudan.edu.cn/stab/help/ original: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76381 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Song_2020_Welch_2019 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Welch, J. D., Kozareva, V., Ferreira, A., Vanderburg, C., Martin, C., & Macosko, E. Z. (2019). Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity. Cell, 177(7), 1873–1887.e17. | https://mai.fudan.edu.cn/stab/help/ original: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126836 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Song_2020_Liu_2016 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Liu, S. J., Nowakowski, T. J., Pollen, A. A., Lui, J. H., Horlbeck, M. A., Attenello, F. J., He, D., Weissman, J. S., Kriegstein, A. R., Diaz, A. A., & Lim, D. A. (2016). Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome biology, 17, 67. | https://mai.fudan.edu.cn/stab/help/ original: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71315 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Song_2020_Onoratu_2016 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Onorati M, Li Z, Liu F, Sousa AMM, Nakagawa N, Li M, Dell'Anno MT, Gulden FO, Pochareddy S, Tebbenkamp ATN, Han W, Pletikos M, Gao T, Zhu Y, Bichsel C, Varela L, Szigeti-Buck K, Lisgo S, Zhang Y, Testen A, Gao XB, Mlakar J, Popovic M, Flamand M, Strittmatter SM, Kaczmarek LK, Anton ES, Horvath TL, Lindenbach BD, Sestan N. Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia. Cell Rep. 2016 Sep 6;16(10):2576-2592 | https://mai.fudan.edu.cn/stab/help/ original: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81475 | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html | Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. |
| Song_2020_Nowakowski_2017 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Nowakowski, T. J., Bhaduri, A., Pollen, A. A., Alvarado, B., Mostajo-Radji, M. A., Di Lullo, E., Haeussler, M., Sandoval-Espinosa, C., Liu, S. J., Velmeshev, D., Ounadjela, J. R., Shuga, J., Wang, X., Lim, D. A., West, J. A., Leyrat, A. A., Kent, W. J., & Kriegstein, A. R. (2017). Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science (New York, N.Y.), 358(6368), 1318–1323. | https://mai.fudan.edu.cn/stab/help/ original: https://cells.ucsc.edu/cortex-dev/exprMatrix.tsv.gz | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://mai.fudan.edu.cn/stab/help/ | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778989/pdf/gkaa762.pdf states: STAB is publicly available at http://stab.comp-sysbio.org. The curated expression and metadata and data grouped by developmental periods, brain regions, and datasets are available at STAB. The raw datasets were obtained with the following link: https://cells.ucsc.edu/cortex-dev/exprMatrix.tsv.gz |
| Song_2020_Habib_2017 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Habib, N., Avraham-Davidi, I., Basu, A., Burks, T., Shekhar, K., Hofree, M., Choudhury, S. R., Aguet, F., Gelfand, E., Ardlie, K., Weitz, D. A., Rozenblatt-Rosen, O., Zhang, F., & Regev, A. (2017). Massively parallel single-nucleus RNA-seq with DroNc-seq. Nature methods, 14(10), 955–958. | https://mai.fudan.edu.cn/stab/help/ original: http://www.gtexportal.org/home/ | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.gtexportal.org/home/license | The GTEx Portal data is made available under the following license: INTRODUCTIONDownloading data from the GTEx Portal servers indicates your acceptance of the following Terms and Conditions: No charges, usage fees or royalties are paid to the GTEx Portal for this data. GENERAL TERMS AND CONDITIONS
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| GTEx_2020 | GTEx Consortium, Laboratory, Data Analysis and Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lead analysts:, Laboratory, Data Analysis &Coordinating Center (LDACC):, NIH program management:, … Montgomery, S. B. (2017). GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science. 2020 Sep 11;369(6509):1318-1330. doi: 10.1126/science.aaz1776. | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://www.gtexportal.org/home/license | The GTEx Portal data is made available under the following license: INTRODUCTIONDownloading data from the GTEx Portal servers indicates your acceptance of the following Terms and Conditions: No charges, usage fees or royalties are paid to the GTEx Portal for this data. GENERAL TERMS AND CONDITIONS
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| Zeisel_2018 | Zeisel, A., Hochgerner, H., Lönnerberg, P., Johnsson, A., Memic, F., van der Zwan, J., Häring, M., Braun, E., Borm, L. E., La Manno, G., Codeluppi, S., Furlan, A., Lee, K., Skene, N., Harris, K. D., Hjerling-Leffler, J., Arenas, E., Ernfors, P., Marklund, U., & Linnarsson, S. (2018). Molecular Architecture of the Mouse Nervous System. Cell, 174(4), 999–1014.e22. | mousebrain.org/adolescent/downloads.html Download: L5_All.loom | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | ||
| Song_2020_Li_2018_Part1 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Li, M., Santpere, G., Imamura Kawasawa, Y., Evgrafov, O. V., Gulden, F. O., Pochareddy, S., Sunkin, S. M., Li, Z., Shin, Y., Zhu, Y., Sousa, A., Werling, D. M., Kitchen, R. R., Kang, H. J., Pletikos, M., Choi, J., Muchnik, S., Xu, X., Wang, D., Lorente-Galdos, B., … Sestan, N. (2018). Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science (New York, N.Y.), 362(6420), eaat7615. | https://mai.fudan.edu.cn/stab/help/ original: http://development.psychencode.org/# | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://mai.fudan.edu.cn/stab/help/ | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778989/pdf/gkaa762.pdf states: STAB is publicly available at http://stab.comp-sysbio.org. The curated expression and metadata and data grouped by developmental periods, brain regions, and datasets are available at STAB. The raw datasets were obtained with the following link: https://cells.ucsc.edu/cortex-dev/exprMatrix.tsv.gz |
| Song_2020_Li_2018_Part2 | Song, L., Pan, S., Zhang, Z., Jia, L., Chen, W. H., & Zhao, X. M. (2021). STAB: a spatio-temporal cell atlas of the human brain. Nucleic acids research, 49(D1), D1029–D1037. and Li, M., Santpere, G., Imamura Kawasawa, Y., Evgrafov, O. V., Gulden, F. O., Pochareddy, S., Sunkin, S. M., Li, Z., Shin, Y., Zhu, Y., Sousa, A., Werling, D. M., Kitchen, R. R., Kang, H. J., Pletikos, M., Choi, J., Muchnik, S., Xu, X., Wang, D., Lorente-Galdos, B., … Sestan, N. (2018). Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science (New York, N.Y.), 362(6420), eaat7615. | https://mai.fudan.edu.cn/stab/help/ original: http://development.psychencode.org/# | Data is aggregated on voxel level, original data can not be retrieved via BrainTrawler | https://mai.fudan.edu.cn/stab/help/ | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778989/pdf/gkaa762.pdf states: STAB is publicly available at http://stab.comp-sysbio.org. The curated expression and metadata and data grouped by developmental periods, brain regions, and datasets are available at STAB. The raw datasets were obtained with the following link: https://cells.ucsc.edu/cortex-dev/exprMatrix.tsv.gz |