{"entity": "researcher", "timestamp": "2026-08-20T20:43:07.770Z", "family": "Kvastad", "given": "Linda", "initials": "L", "orcid": "0000-0001-5869-3485", "affiliations": ["Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/384e05b0be164cabb26bc3ce544742db.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/384e05b0be164cabb26bc3ce544742db"}}, "publications": [{"entity": "publication", "iuid": "1fd63b9e22274e52a89452c122fff95c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1fd63b9e22274e52a89452c122fff95c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1fd63b9e22274e52a89452c122fff95c"}}, "title": "Spatial transcriptomics and genetically implicated genes identify putative causal tissue structures for complex traits", "authors": [{"family": "Kvastad", "given": "Linda", "initials": "L", "orcid": "0000-0001-5869-3485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/384e05b0be164cabb26bc3ce544742db.json"}}, {"family": "Kollotzek", "given": "Aaron", "initials": "A", "orcid": "0009-0009-7142-4015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e3e7078a9844e20a99d7e6fdaea697a.json"}}, {"family": "Saghaleyni", "given": "Rasool", "initials": "R", "orcid": "0000-0003-0956-039X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/323805f055b44e208905ef70acbf6cc4.json"}}, {"family": "Chang", "given": "Chih Fan", "initials": "CF", "orcid": "0009-0003-1944-0823", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0074f52d87c9499096d4d2d582d5b65a.json"}}, {"family": "Cao", "given": "Tianze", "initials": "T", "orcid": "0009-0009-6674-740X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ce744c149e4f729c5930c3be6eef4d.json"}}, {"family": "Lappalainen", "given": "Tuuli", "initials": "T", "orcid": "0000-0002-7746-8109", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8401dbf3ffb4f35bcc8e16f4a04cd7c.json"}}], "type": "posted-content", "published": "2025-05-02", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.05.02.651876", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:02:44.272Z", "modified": "2026-08-20T11:04:58.778Z"}, {"entity": "publication", "iuid": "3adaf7e2d1d14eb7bb027bb18463c836", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3adaf7e2d1d14eb7bb027bb18463c836.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3adaf7e2d1d14eb7bb027bb18463c836"}}, "title": "Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples.", "authors": [{"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ad34c94b64432ab74d61fbc6d16905.json"}}, {"family": "Newton", "given": "Phillip T", "initials": "PT", "orcid": "0000-0003-2142-1798", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e490d4b3da4741b490395399f1b8c1.json"}}, {"family": "Galicia", "given": "Leire Alonso", "initials": "LA"}, {"family": "Abalo", "given": "Xes\u00fas M", "initials": "XM", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb96c37f02b45d290b89f5b615052df.json"}}, {"family": "Avijgan", "given": "Mahtab", "initials": "M"}, {"family": "Kvastad", "given": "Linda", "initials": "L", "orcid": "0000-0001-5869-3485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/384e05b0be164cabb26bc3ce544742db.json"}}, {"family": "Denadai-Souza", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-0385-1321", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4f2a0f8d4d6470d8cf48d3a27b19b78.json"}}, {"family": "Stakenborg", "given": "Nathalie", "initials": "N", "orcid": "0000-0002-6229-0045", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d107940932374682934e1ee3860c20f2.json"}}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB"}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Jurek", "given": "Aleksandra", "initials": "A"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ff9fe255d640c0a2bbed0913fe208d.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C"}, {"family": "Boeckxstaens", "given": "Guy", "initials": "G", "orcid": "0000-0001-8267-5797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a5224f2c1014dab80a2e50af25d7a18.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}], "type": "journal article", "published": "2023-01-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "509", "issn-l": "2041-1723"}, "abstract": "Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins.", "doi": "10.1038/s41467-023-36071-5", "pmid": "36720873", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9889806"}, {"db": "pii", "key": "10.1038/s41467-023-36071-5"}], "notes": [], "created": "2026-08-20T08:52:29.319Z", "modified": "2026-08-20T08:52:29.623Z"}, {"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"}]}