{"entity": "researcher", "timestamp": "2026-05-12T21:31:25.142Z", "family": "Klughammer", "given": "J", "initials": "J", "orcid": "0000-0002-3628-9278", "affiliations": ["Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e55a4df3bef48e1a3980d9186dbe987.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e55a4df3bef48e1a3980d9186dbe987"}}, "publications": [{"entity": "publication", "iuid": "ab667d31fb0e4bbeb87d2e9af420d3ab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ab667d31fb0e4bbeb87d2e9af420d3ab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ab667d31fb0e4bbeb87d2e9af420d3ab"}}, "title": "SM-Omics is an automated platform for high-throughput spatial multi-omics.", "authors": [{"family": "Vickovic", "given": "S", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d4188f01ed74ba499ef845e0ad9fe97.json"}}, {"family": "L\u00f6tstedt", "given": "B", "initials": "B", "orcid": "0000-0003-3545-5489", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5865e21892fd48e09972aca7b3d11d9b.json"}}, {"family": "Klughammer", "given": "J", "initials": "J", "orcid": "0000-0002-3628-9278", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e55a4df3bef48e1a3980d9186dbe987.json"}}, {"family": "Mages", "given": "S", "initials": "S"}, {"family": "Segerstolpe", "given": "\u00c5", "initials": "\u00c5"}, {"family": "Rozenblatt-Rosen", "given": "O", "initials": "O", "orcid": "0000-0001-6313-3570", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d219a623b5d4e46af7841b1f32036c3.json"}}, {"family": "Regev", "given": "A", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca26c12602774846b5d8156baf52dfb6.json"}}], "type": "journal article", "published": "2022-02-10", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "795", "issn-l": "2041-1723"}, "abstract": "The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial transcriptomics has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. Here, we advance the application of spatial transcriptomics at scale, by presenting Spatial Multi-Omics (SM-Omics) as a fully automated, high-throughput all-sequencing based platform for combined and spatially resolved transcriptomics and antibody-based protein measurements. SM-Omics uses DNA-barcoded antibodies, immunofluorescence or a combination thereof, to scale and combine spatial transcriptomics and spatial antibody-based multiplex protein detection. SM-Omics allows processing of up to 64 in situ spatial reactions or up to 96 sequencing-ready libraries, of high complexity, in a ~2 days process. We demonstrate SM-Omics in the mouse brain, spleen and colorectal cancer model, showing its broad utility as a high-throughput platform for spatial multi-omics.", "doi": "10.1038/s41467-022-28445-y", "pmid": "35145087", "labels": {"Sanja Vickovic": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8831571"}, {"db": "pii", "key": "10.1038/s41467-022-28445-y"}], "notes": [], "created": "2023-12-03T15:46:04.963Z", "modified": "2023-12-03T15:46:05.108Z"}, {"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"}]}