{"entity": "researcher", "timestamp": "2026-07-20T13:12:01.747Z", "family": "Gyllborg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1429-6426", "affiliations": ["Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/a5c0db7c1c9b474b8726fbd44d530330.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/a5c0db7c1c9b474b8726fbd44d530330"}}, "publications": [{"entity": "publication", "iuid": "151d85634a7c4b3f91ab1db716346e7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/151d85634a7c4b3f91ab1db716346e7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/151d85634a7c4b3f91ab1db716346e7f"}}, "title": "Comprehensive in situ mapping of human cortical transcriptomic cell types.", "authors": [{"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM", "orcid": "0000-0003-2230-8594", "researcher": {"href": "https://publications.scilifelab.se/researcher/df19aaf2ad714a63aa40dc6b18a06229.json"}}, {"family": "Gyllborg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1429-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5c0db7c1c9b474b8726fbd44d530330.json"}}, {"family": "Miller", "given": "Jeremy A", "initials": "JA", "orcid": "0000-0003-4549-588X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa758938d296460c8066cc14376896d3.json"}}, {"family": "Close", "given": "Jennie L", "initials": "JL"}, {"family": "Long", "given": "Brian", "initials": "B", "orcid": "0000-0002-7793-5969", "researcher": {"href": "https://publications.scilifelab.se/researcher/19069749bcda42d683765351e485d984.json"}}, {"family": "Lein", "given": "Ed S", "initials": "ES", "orcid": "0000-0001-9012-6552", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dd450c764a4431aa798630053343cd6.json"}}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de5317c53f34bc89dabfddb0be44983.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "journal article", "published": "2021-08-24", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "998", "issn-l": "2399-3642"}, "abstract": "The ability to spatially resolve the cellular architecture of human cortical cell types over informative areas is essential to understanding brain function. We combined in situ sequencing gene expression data and single-nucleus RNA-sequencing cell type definitions to spatially map cells in sections of the human cortex via probabilistic cell typing. We mapped and classified a total of 59,816 cells into all 75 previously defined subtypes to create a first spatial atlas of human cortical cells in their native position, their abundances and genetic signatures. We also examined the precise within- and across-layer distributions of all the cell types and provide a resource for the cell atlas community. The abundances and locations presented here could serve as a reference for further studies, that include human brain tissues and disease applications at the cell type level.", "doi": "10.1038/s42003-021-02517-z", "pmid": "34429496", "labels": {"In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02517-z"}, {"db": "pmc", "key": "PMC8384853"}], "notes": [], "created": "2021-12-10T17:13:17.226Z", "modified": "2025-10-17T13:02:17.907Z"}, {"entity": "publication", "iuid": "aac00ea44cb647ffb44382c885f897a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aac00ea44cb647ffb44382c885f897a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aac00ea44cb647ffb44382c885f897a2"}}, "title": "Molecular architecture of the developing mouse brain.", "authors": [{"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Siletti", "given": "Kimberly", "initials": "K"}, {"family": "Furlan", "given": "Alessandro", "initials": "A"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1429-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5c0db7c1c9b474b8726fbd44d530330.json"}}, {"family": "Vinsland", "given": "Elin", "initials": "E"}, {"family": "Mossi Albiach", "given": "Alejandro", "initials": "A", "orcid": "0000-0001-7009-4901", "researcher": {"href": "https://publications.scilifelab.se/researcher/71fd1a6c4e174f27b2e25a24732838d0.json"}}, {"family": "Mattsson Langseth", "given": "Christoffer", "initials": "C", "orcid": "0000-0003-2230-8594", "researcher": {"href": "https://publications.scilifelab.se/researcher/df19aaf2ad714a63aa40dc6b18a06229.json"}}, {"family": "Khven", "given": "Irina", "initials": "I"}, {"family": "Lederer", "given": "Alex R", "initials": "AR"}, {"family": "Dratva", "given": "Lisa M", "initials": "LM", "orcid": "0000-0002-2873-6787", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ff74c24d9a4f71b6684d2eb3d177db.json"}}, {"family": "Johnsson", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "596", "issue": "7870", "pages": "92-96", "issn-l": "0028-0836"}, "abstract": "The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell-cell interactions and intrinsic genetic programs that result in probably more than a thousand distinct cell types. A complete understanding of this process requires a systematic characterization of cell states over the entire spatiotemporal range of brain development. The ability of single-cell RNA sequencing and spatial transcriptomics to reveal the molecular heterogeneity of complex tissues has therefore been particularly powerful in the nervous system. Previous studies have explored development in specific brain regions1-8, the whole adult brain9 and even entire embryos10. Here we report a comprehensive single-cell transcriptomic atlas of the embryonic mouse brain between gastrulation and birth. We identified almost eight hundred cellular states that describe a developmental program for the functional elements of the brain and its enclosing membranes, including the early neuroepithelium, region-specific secondary organizers, and both neurogenic and gliogenic progenitors. We also used in situ mRNA sequencing to map the spatial expression patterns of key developmental genes. Integrating the in situ data with our single-cell clusters revealed the precise spatial organization of neural progenitors during the patterning of the nervous system.", "doi": "10.1038/s41586-021-03775-x", "pmid": "34321664", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03775-x"}], "notes": [], "created": "2021-10-01T09:03:14.935Z", "modified": "2025-10-17T13:02:17.936Z"}, {"entity": "publication", "iuid": "207936006e674630a3c278932612d8b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/207936006e674630a3c278932612d8b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/207936006e674630a3c278932612d8b8"}}, "title": "Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.", "authors": [{"family": "Gyllborg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1429-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5c0db7c1c9b474b8726fbd44d530330.json"}}, {"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X"}, {"family": "Choi", "given": "Eunkyoung", "initials": "E"}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM"}, {"family": "Hilscher", "given": "Markus M", "initials": "MM"}, {"family": "Lein", "given": "Ed S", "initials": "ES"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "journal article", "published": "2020-11-04", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "48", "issue": "19", "pages": "e112"}, "abstract": "Visualization of the transcriptome in situ has proven to be a valuable tool in exploring single-cell RNA-sequencing data, providing an additional spatial dimension to investigate multiplexed gene expression, cell types, disease architecture or even data driven discoveries. In situ sequencing (ISS) method based on padlock probes and rolling circle amplification has been used to spatially resolve gene transcripts in tissue sections of various origins. Here, we describe the next iteration of ISS, HybISS, hybridization-based in situ sequencing. Modifications in probe design allows for a new barcoding system via sequence-by-hybridization chemistry for improved spatial detection of RNA transcripts. Due to the amplification of probes, amplicons can be visualized with standard epifluorescence microscopes for high-throughput efficiency and the new sequencing chemistry removes limitations bound by sequence-by-ligation chemistry of ISS. HybISS design allows for increased flexibility and multiplexing, increased signal-to-noise, all without compromising throughput efficiency of imaging large fields of view. Moreover, the current protocol is demonstrated to work on human brain tissue samples, a source that has proven to be difficult to work with image-based spatial analysis techniques. Overall, HybISS technology works as a targeted amplification detection method for improved spatial transcriptomic visualization, and importantly, with an ease of implementation.", "doi": "10.1093/nar/gkaa792", "pmid": "32990747", "labels": {"Bioinformatics Support for Computational Resources": "Service", "In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pii", "key": "5912821"}, {"db": "pmc", "key": "PMC7641728"}], "notes": [], "created": "2020-12-11T18:51:33.812Z", "modified": "2025-10-17T13:02:18.129Z"}]}