[ { "id": "https://authors.library.caltech.edu/records/sr2rf-e0549", "eprint_id": 108898, "eprint_status": "archive", "datestamp": "2023-08-20 02:49:37", "lastmod": "2023-12-13 16:45:51", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Takei-Yodai", "name": { "family": "Takei", "given": "Yodai" } }, { "id": "Zheng-Shiwei", "name": { "family": "Zheng", "given": "Shiwei" }, "orcid": "0000-0001-6682-6743" }, { "id": "Yun-Jina", "name": { "family": "Yun", "given": "Jina" } }, { "id": "Shah-Sheel", "name": { "family": "Shah", "given": "Sheel" } }, { "id": "Pierson-Nico-G", "name": { "family": "Pierson", "given": "Nico" }, "orcid": "0000-0002-2451-0633" }, { "id": "White-Joanthan-A", "name": { "family": "White", "given": "Jonathan" }, "orcid": "0000-0002-7009-3332" }, { "id": "Schindler-Simone", "name": { "family": "Schindler", "given": "Simone" } }, { "id": "Tischbirek-Carsten", "name": { "family": "Tischbirek", "given": "Carsten" } }, { "id": "Yuan-Guo-Cheng", "name": { "family": "Yuan", "given": "Guo-Cheng" }, "orcid": "0000-0002-2283-4714" }, { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" } ] }, "title": "Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architecture", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nThis version posted April 27, 2021. \n\nWe thank N. Ollikainen and M. Guttman for help with Hi-C analysis; R.J. Oakey for providing the processed ChIP-seq data; C.-H.L. Eng for helpful discussion; C. Karp for making custom-made flow cells; L. Sanchez and E. Buitrago-Delgado for help with the perfusion setup; I. Strazhnik for help with figures; A. Anderson for help with the manuscript. \n\nThis work was supported by NIH 4DN DA047732 and supplement (L.C.), and the Paul G. Allen Frontiers Foundation Discovery Center (L.C.). \n\nAuthor contributions: Y.T. and L.C. conceived the idea and designed experiments. Y.T. designed probes with input from C.T.. Y.T., J.Y., and S.Schindler prepared and validated experimental materials. Y.T. performed imaging experiments. Y.T., S.Shah., N.P., and J.W. wrote image processing scripts, and Y.T. performed image processing. Y.T., S.Z., and L.C. analysed data with input from G.-C.Y.. Y.T. and L.C. wrote the manuscript with input from S.Z., C.T., and G.-C.Y.. L.C. supervised all aspects of the projects. \n\nCompeting interests: L.C. is a co-founder of Spatial Genomics Inc. \n\nData and materials availability: The custom written scripts used in this study are available in a Github repository (https://github.com/CaiGroup/dna-seqfish-plus-tissue). The source data and processed data from this study are available in a Zenodo repository (55).\n\n
Submitted - 2021.04.26.441547v1.full.pdf
Supplemental Material - media-1.xlsx
Supplemental Material - media-2.xlsx
Supplemental Material - media-3.xlsx
Supplemental Material - media-4.csv
", "abstract": "Nuclear architecture in tissues can arise from cell-type specific organization of nuclear bodies, chromatin states and chromosome structures. However, the lack of genome-wide measurements to interrelate such modalities within single cells limits our overall understanding of nuclear architecture. Here, we demonstrate integrated spatial genomics in the mouse brain cortex, imaging thousands of genomic loci along with RNAs and subnuclear markers simultaneously in individual cells. We revealed chromatin fixed points, combined with cell-type specific organization of nuclear bodies, arrange the interchromosomal organization and radial positioning of chromosomes in diverse cell types. At the sub-megabase level, we uncovered a collection of single-cell chromosome domain structures, including those for the active and inactive X chromosomes. These results advance our understanding of single-cell nuclear architecture in complex tissues.", "date": "2021-04-30", "date_type": "published", "id_number": "CaltechAUTHORS:20210430-091508303", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210430-091508303", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "4DN DA047732" }, { "agency": "Paul G. Allen Family Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.04.26.441547", "primary_object": { "basename": "media-1.xlsx", "url": "https://authors.library.caltech.edu/records/sr2rf-e0549/files/media-1.xlsx" }, "related_objects": [ { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/sr2rf-e0549/files/media-2.xlsx" }, { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/sr2rf-e0549/files/media-3.xlsx" }, { "basename": "media-4.csv", "url": "https://authors.library.caltech.edu/records/sr2rf-e0549/files/media-4.csv" }, { "basename": "2021.04.26.441547v1.full.pdf", "url": "https://authors.library.caltech.edu/records/sr2rf-e0549/files/2021.04.26.441547v1.full.pdf" } ], "resource_type": "monograph", "pub_year": "2021", "author_list": "Takei, Yodai; Zheng, Shiwei; et el." }, { "id": "https://authors.library.caltech.edu/records/ah4qa-qnq68", "eprint_id": 89047, "eprint_status": "archive", "datestamp": "2023-08-19 08:13:27", "lastmod": "2023-10-20 21:53:35", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhu-Qian", "name": { "family": "Zhu", "given": "Qian" } }, { "id": "Shah-Sheel", "name": { "family": "Shah", "given": "Sheel" } }, { "id": "Dries-R", "name": { "family": "Dries", "given": "Ruben" } }, { "id": "Cai-Long", "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "id": "Yuan-Guo-Cheng", "name": { "family": "Yuan", "given": "Guo-Cheng" }, "orcid": "0000-0002-2283-4714" } ] }, "title": "Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nbioRxiv preprint first posted online Mar. 2, 2018. \n\nCode Availability: Code is deposited at https://bitbucket.org/qzhu/smfish-hmrf. \n\nData Availability: Expression data, spatial coordinates, SVM prediction results and HMRF segmentation results are deposited at https://bitbucket.org/qzhu/smfish-hmrf. \n\nAnimal research was conducted in compliance with all relevant ethical regulations and other institutional requirements.\n\nSubmitted - 275156.full.pdf
", "abstract": "Both the intrinsic regulatory network and spatial environment are contributors of cellular identity and result in cell state variations. However, their individual contributions remain poorly understood. Here we present a systematic approach to integrate both sequencing- and imaging-based single-cell transcriptomic profiles, thereby combining whole-transcriptomic and spatial information from these assays. We applied this approach to dissect the cell-type and spatial domain associated heterogeneity within the mouse visual cortex region. Our analysis identified distinct spatially associated signatures within glutamatergic and astrocyte cell compartments, indicating strong interactions between cells and their surrounding environment. Using these signatures as a guide to analyze single cell RNAseq data, we identified previously unknown, but spatially associated subpopulations. As such, our integrated approach provides a powerful tool for dissecting the roles of intrinsic regulatory networks and spatial environment in the maintenance of cellular states.", "date": "2018-08-22", "date_type": "published", "id_number": "CaltechAUTHORS:20180822-140737502", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180822-140737502", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1101/275156", "primary_object": { "basename": "275156.full.pdf", "url": "https://authors.library.caltech.edu/records/ah4qa-qnq68/files/275156.full.pdf" }, "resource_type": "monograph", "pub_year": "2018", "author_list": "Zhu, Qian; Shah, Sheel; et el." } ]