دورية أكاديمية
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.
| العنوان: | Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. |
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| المؤلفون: | Biancalani T; Broad Institute of MIT and Harvard, Cambridge, MA, USA. tommaso.biancalani@gmail.com.; Genentech, South San Francisco, CA, USA. tommaso.biancalani@gmail.com., Scalia G; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Roche, Monza, Italy., Buffoni L; Department of Physics and Astrophysics, University of Florence, Florence, Italy., Avasthi R; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Northeastern University, Boston, MA, USA., Lu Z; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Northeastern University, Boston, MA, USA., Sanger A; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Tokcan N; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Vanderburg CR; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Segerstolpe Å; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Zhang M; Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA., Avraham-Davidi I; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Vickovic S; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Nitzan M; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.; School of Computer Science and Engineering, Racah Institute of Physics, Faculty of Medicine, The Hebrew University, Jerusalem, Israel., Ma S; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Biology, MIT, Cambridge, MA, USA.; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA., Subramanian A; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Lipinski M; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA., Buenrostro J; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA., Brown NB; Northeastern University, Boston, MA, USA., Fanelli D; Department of Physics and Astrophysics, University of Florence, Florence, Italy., Zhuang X; Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA., Macosko EZ; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Regev A; Broad Institute of MIT and Harvard, Cambridge, MA, USA. aviv.regev.sc@gmail.com.; Department of Biology, MIT, Cambridge, MA, USA. aviv.regev.sc@gmail.com.; Genentech, South San Francisco, CA, USA. aviv.regev.sc@gmail.com.; Howard Hughes Medical Institute, Chevy Chase, MD, USA. aviv.regev.sc@gmail.com. |
| المصدر: | Nature methods [Nat Methods] 2021 Nov; Vol. 18 (11), pp. 1352-1362. Date of Electronic Publication: 2021 Oct 28. |
| نوع المنشور: | Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: New York, NY : Nature Pub. Group, c2004- |
| مواضيع طبية MeSH: | Deep Learning* , Gene Expression Regulation* , Software* , Transcriptome*, Brain/*metabolism , Chromatin/*genetics , Single-Cell Analysis/*methods, Animals ; Chromatin/chemistry ; Chromatin/metabolism ; Female ; Gene Expression Profiling ; Male ; Mice ; Mice, Inbred C57BL ; RNA-Seq ; Regulatory Sequences, Nucleic Acid |
| مستخلص: | Charting an organs' biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for spatial measurements, but at lower resolution and with limited sensitivity. Targeted in situ technologies solve both issues, but are limited in gene throughput. To overcome these limitations we present Tangram, a method that aligns sc/snRNA-seq data to various forms of spatial data collected from the same region, including MERFISH, STARmap, smFISH, Spatial Transcriptomics (Visium) and histological images. Tangram can map any type of sc/snRNA-seq data, including multimodal data such as those from SHARE-seq, which we used to reveal spatial patterns of chromatin accessibility. We demonstrate Tangram on healthy mouse brain tissue, by reconstructing a genome-wide anatomically integrated spatial map at single-cell resolution of the visual and somatomotor areas. (© 2021. The Author(s).) |
| التعليقات: | Comment in: Nat Methods. 2021 Nov;18(11):1282-1283. (PMID: 34711969) |
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| معلومات مُعتمدة: | OT2 OD026673 United States OD NIH HHS; U19 MH114821 United States MH NIMH NIH HHS; U19 MH114830 United States MH NIMH NIH HHS; United States HHMI Howard Hughes Medical Institute |
| المشرفين على المادة: | 0 (Chromatin) |
| تواريخ الأحداث: | Date Created: 20211029 Date Completed: 20211228 Latest Revision: 20240404 |
| رمز التحديث: | 20240404 |
| مُعرف محوري في PubMed: | PMC8566243 |
| DOI: | 10.1038/s41592-021-01264-7 |
| PMID: | 34711971 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1548-7105 |
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| DOI: | 10.1038/s41592-021-01264-7 |