{"entity": "researcher", "timestamp": "2026-09-05T18:05:43.115Z", "family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "affiliations": ["Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/42b9688e2b634ae5b40b28b2ff23f9ee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/42b9688e2b634ae5b40b28b2ff23f9ee"}}, "publications": [{"entity": "publication", "iuid": "853fe45e2b8946ae9102a32e2959eb18", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/853fe45e2b8946ae9102a32e2959eb18.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/853fe45e2b8946ae9102a32e2959eb18"}}, "title": "The spatial RNA integrity number assay for in situ evaluation of transcriptome quality.", "authors": [{"family": "Kvastad", "given": "Linda", "initials": "L", "orcid": "0000-0001-5869-3485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/384e05b0be164cabb26bc3ce544742db.json"}}, {"family": "Carlberg", "given": "Konstantin", "initials": "K"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Villacampa", "given": "Eva Gracia", "initials": "EG", "orcid": "0000-0003-0353-2101", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35a5dafa84024d5e82eb8f14632a3cf6.json"}}, {"family": "Stuckey", "given": "Alexander", "initials": "A"}, {"family": "Stenbeck", "given": "Linnea", "initials": "L", "orcid": "0000-0002-0210-7886", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b2de0dae49f4ab39d45281316703ca9.json"}}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Zamboni", "given": "Margherita", "initials": "M", "orcid": "0000-0003-0664-4707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dd167b1cb344898bccd0d60315db61c.json"}}, {"family": "Magnusson", "given": "Jens Peter", "initials": "JP", "orcid": "0000-0002-3928-8959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc0f61d71be8461c8ad475e14311e7ba.json"}}, {"family": "Basmaci", "given": "Elisa", "initials": "E"}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Prochazka", "given": "Gabriela", "initials": "G"}, {"family": "Schaupp", "given": "Anna-Lena", "initials": "AL"}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42b9688e2b634ae5b40b28b2ff23f9ee.json"}}, {"family": "Fugger", "given": "Lars", "initials": "L"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ff9fe255d640c0a2bbed0913fe208d.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}], "type": "evaluation study", "published": "2021-01-08", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "57", "issn-l": "2399-3642"}, "abstract": "The RNA integrity number (RIN) is a frequently used quality metric to assess the completeness of rRNA, as a proxy for the corresponding mRNA in a tissue. Current methods operate at bulk resolution and provide a single average estimate for the whole sample. Spatial transcriptomics technologies have emerged and shown their value by placing gene expression into a tissue context, resulting in transcriptional information from all tissue regions. Thus, the ability to estimate RNA quality in situ has become of utmost importance to overcome the limitation with a bulk rRNA measurement. Here we show a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at cellular resolution. We demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows.", "doi": "10.1038/s42003-020-01573-1", "pmid": "33420318", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7794352"}, {"db": "pii", "key": "10.1038/s42003-020-01573-1"}], "notes": [], "created": "2026-08-20T09:24:57.181Z", "modified": "2026-08-20T09:24:57.385Z"}, {"entity": "publication", "iuid": "413667177e38441d83731b8db1d07378", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/413667177e38441d83731b8db1d07378.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/413667177e38441d83731b8db1d07378"}}, "title": "High-definition spatial transcriptomics for in situ tissue profiling.", "authors": [{"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4188f01ed74ba499ef845e0ad9fe97.json"}}, {"family": "Eraslan", "given": "G\u00f6kcen", "initials": "G", "orcid": "0000-0001-9579-2909", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fcbc1d88c5f0403597ae9ad724de6548.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Klughammer", "given": "Johanna", "initials": "J", "orcid": "0000-0002-3628-9278", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e55a4df3bef48e1a3980d9186dbe987.json"}}, {"family": "Stenbeck", "given": "Linnea", "initials": "L", "orcid": "0000-0002-0210-7886", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b2de0dae49f4ab39d45281316703ca9.json"}}, {"family": "Schapiro", "given": "Denis", "initials": "D"}, {"family": "\u00c4ij\u00f6", "given": "Tarmo", "initials": "T", "orcid": "0000-0002-3008-4634", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1b52cf5dea442c6bbee87f3507cadb4.json"}}, {"family": "Bonneau", "given": "Richard", "initials": "R"}, {"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L", "orcid": "0000-0002-5108-4481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60ea7a079ae04b8896196dafec84a6fc.json"}}, {"family": "Navarro", "given": "Jos\u00e9 Fernand\u00e9z", "initials": "JF", "orcid": "0000-0002-4035-5258", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c9e34949eec41deba11bc669e9217b0.json"}}, {"family": "Gould", "given": "Joshua", "initials": "J", "orcid": "0000-0001-9581-5461", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f52ad057c7fe4c8cadddd38e63679ddd.json"}}, {"family": "Griffin", "given": "Gabriel K", "initials": "GK", "orcid": "0000-0002-4042-6757", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6153204e19d4660b640dc4467605973.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42b9688e2b634ae5b40b28b2ff23f9ee.json"}}, {"family": "Ronaghi", "given": "Mostafa", "initials": "M"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Regev", "given": "Aviv", "initials": "A"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/132000c8241249d9b2c4cfeb4a058862.json"}}], "type": "journal article", "published": "2019-10-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "16", "issue": "10", "pages": "987-990", "issn-l": "1548-7091"}, "abstract": "Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures RNA from histological tissue sections on a dense, spatially barcoded bead array. Each experiment recovers several hundred thousand transcript-coupled spatial barcodes at 2-\u03bcm resolution, as demonstrated in mouse brain and primary breast cancer. This opens the way to high-resolution spatial analysis of cells and tissues.", "doi": "10.1038/s41592-019-0548-y", "pmid": "31501547", "labels": {"Sanja Vickovic": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1536533"}, {"db": "pmc", "key": "PMC6765407"}, {"db": "pii", "key": "10.1038/s41592-019-0548-y"}], "notes": [], "created": "2023-12-03T15:47:14.726Z", "modified": "2023-12-03T15:47:15.055Z"}]}