{"entity": "researcher", "timestamp": "2026-06-10T00:33:02.324Z", "family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "affiliations": ["Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. nicola.crosetto@ki.se.", "Science for Life Laboratory, Stockholm, Sweden. nicola.crosetto@ki.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3"}}, "publications": [{"entity": "publication", "iuid": "8878962be50c44d791a0589626c424a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8878962be50c44d791a0589626c424a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8878962be50c44d791a0589626c424a7"}}, "title": "Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.", "authors": [{"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Gelali", "given": "Eleni", "initials": "E"}, {"family": "Girelli", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-4264-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/a607510e88954d0980e1d4505ab27ee7.json"}}, {"family": "Wang", "given": "Su", "initials": "S"}, {"family": "Castillo", "given": "David", "initials": "D", "orcid": "0000-0003-0478-0828", "researcher": {"href": "https://publications.scilifelab.se/researcher/2430e6a8b8b341f18566cca62c27cc6d.json"}}, {"family": "Mattsson Langseth", "given": "Christoffer", "initials": "C"}, {"family": "Verron", "given": "Quentin", "initials": "Q"}, {"family": "Nguyen", "given": "Huy Q", "initials": "HQ"}, {"family": "Chattoraj", "given": "Shyamtanu", "initials": "S"}, {"family": "Martinez Casals", "given": "Anna", "initials": "A"}, {"family": "Blom", "given": "Hans", "initials": "H"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Marti-Renom", "given": "Marc A", "initials": "MA"}, {"family": "Wu", "given": "Chao-Ting", "initials": "C"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2024-06-06", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "issn-l": "1548-7091", "volume": null, "issue": null, "pages": null}, "abstract": "Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of extractable biological information. To overcome these limitations, here we develop Deconwolf, an open-source, user-friendly software for high-performance deconvolution of widefield fluorescence microscopy images, which efficiently runs on laptop computers. Deconwolf enables accurate quantification of crowded diffraction limited fluorescence dots in DNA and RNA fluorescence in situ hybridization images and allows robust detection of individual transcripts in tissue sections imaged with \u00d720 air objectives. Deconvolution of in situ spatial transcriptomics images with Deconwolf increased the number of transcripts identified more than threefold, while the application of Deconwolf to images obtained by fluorescence in situ sequencing of barcoded Oligopaint probes drastically improved chromosome tracing. Deconwolf greatly facilitates the use of deconvolution in many bioimaging applications.", "doi": "10.1038/s41592-024-02294-7", "pmid": "38844629", "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development", "Spatial Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-024-02294-7"}], "notes": [], "created": "2024-06-10T07:36:02.247Z", "modified": "2024-11-25T17:49:12.405Z"}, {"entity": "publication", "iuid": "8acfeb033c3c459a9cff10bf8bb576c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8acfeb033c3c459a9cff10bf8bb576c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8acfeb033c3c459a9cff10bf8bb576c9"}}, "title": "High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue.", "authors": [{"family": "Zhang", "given": "Ning", "initials": "N"}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Verron", "given": "Quentin", "initials": "Q"}, {"family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}}, {"family": "Bellomo", "given": "Sara E", "initials": "SE"}, {"family": "Longo", "given": "Gabriel M C", "initials": "GMC", "orcid": "0000-0003-2028-1068", "researcher": {"href": "https://publications.scilifelab.se/researcher/2afe47a108d0451ebaf8269a0f18eb84.json"}}, {"family": "Ratz", "given": "Michael", "initials": "M", "orcid": "0000-0002-9795-8033", "researcher": {"href": "https://publications.scilifelab.se/researcher/a481899ca58a467499f56af4feb5457c.json"}}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Su", "given": "Peng", "initials": "P"}, {"family": "Han", "given": "Bo", "initials": "B"}, {"family": "Wang", "given": "Wanzhong", "initials": "W"}, {"family": "Onorato", "given": "Sofia", "initials": "S"}, {"family": "Grassini", "given": "Dora", "initials": "D"}, {"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Giordano", "given": "Silvia", "initials": "S", "orcid": "0000-0003-1854-1086", "researcher": {"href": "https://publications.scilifelab.se/researcher/7072fc7ce1d44d0392b4ba3da82a16fb.json"}}, {"family": "Yang", "given": "Qifeng", "initials": "Q"}, {"family": "Sapino", "given": "Anna", "initials": "A", "orcid": "0000-0003-3542-9571", "researcher": {"href": "https://publications.scilifelab.se/researcher/b77045e1832b4267b330df154cbe80db.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Druid", "given": "Henrik", "initials": "H", "orcid": "0000-0002-9198-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bb7f9c706b451f9813bae017e0fad7.json"}}, {"family": "Roukos", "given": "Vassilis", "initials": "V", "orcid": "0000-0002-5065-3937", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5da3165b15741ff967e77618bd96cc1.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2024-04-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3475", "issn-l": "2041-1723"}, "abstract": "Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly characterized. Here, we perform multi-region, single-cell DNA sequencing to characterize the SCNA landscape across tumor-rich and normal tissue in two male patients with localized prostate cancer. We identify two distinct karyotypes: 'pseudo-diploid' cells harboring few SCNAs and highly aneuploid cells. Pseudo-diploid cells form numerous small-sized subclones ranging from highly spatially localized to broadly spread subclones. In contrast, aneuploid cells do not form subclones and are detected throughout the prostate, including normal tissue regions. Highly localized pseudo-diploid subclones are confined within tumor-rich regions and carry deletions in multiple tumor-suppressor genes. Our study reveals that SCNAs are widespread in normal and tumor regions across the prostate in localized prostate cancer patients and suggests that a subset of pseudo-diploid cells drive tumorigenesis in the aging prostate.", "doi": "10.1038/s41467-024-47664-z", "pmid": "38658552", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11043350"}, {"db": "pii", "key": "10.1038/s41467-024-47664-z"}], "notes": [], "created": "2024-05-17T09:16:39.558Z", "modified": "2024-11-25T10:16:43.449Z"}, {"entity": "publication", "iuid": "80c75635458e45f883e80acd6b1c4fc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80c75635458e45f883e80acd6b1c4fc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80c75635458e45f883e80acd6b1c4fc1"}}, "title": "scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.", "authors": [{"family": "Chen", "given": "Jinxin Phaedo", "initials": "JP", "orcid": "0000-0002-0729-5214", "researcher": {"href": "https://publications.scilifelab.se/researcher/25fca568763f4476b53bdf7297689a2e.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Wu", "given": "Honggui", "initials": "H", "orcid": "0000-0001-7880-0591", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9697e391fe493ab4b26d2c40e7565f.json"}}, {"family": "Chen", "given": "Chong", "initials": "C", "orcid": "0000-0002-6787-0495", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8a6778068124d7cb3dd1aca6e7cc0ec.json"}}, {"family": "Della Chiara", "given": "Giulia", "initials": "G", "orcid": "0000-0001-5211-3814", "researcher": {"href": "https://publications.scilifelab.se/researcher/3410a95b5b674fa69d2c83b479d345a8.json"}}, {"family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}}, {"family": "Georgiadis", "given": "Konstantinos L", "initials": "KL"}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM"}, {"family": "Virdi", "given": "Mohit", "initials": "M"}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Bellomo", "given": "Sara Erika", "initials": "SE"}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1768", "issn-l": "2041-1723"}, "abstract": "Extrachromosomal circular DNAs (eccDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for profiling eccDNAs and unraveling their diversity and complexity in single cells. We implement and validate scCircle-seq in normal and cancer cell lines, demonstrating that most eccDNAs vary largely between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. eccDNAs are preferentially produced from chromatin regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress conditions. Concomitant sequencing of eccDNAs and RNA from the same cell uncovers the absence of correlation between eccDNA copy number and gene expression levels, except for a few oncogenes, including MYC, contained within a large eccDNA in colorectal cancer cells. Lastly, we apply scCircle-seq to one prostate cancer and two breast cancer specimens, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, and further expands the potential of eccDNAs for cancer diagnostics.", "doi": "10.1038/s41467-024-45972-y", "pmid": "38409079", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10897160"}, {"db": "pii", "key": "10.1038/s41467-024-45972-y"}], "notes": [], "created": "2024-03-14T11:05:03.191Z", "modified": "2024-04-26T09:08:57.780Z"}, {"entity": "publication", "iuid": "34c38b3d3f564542956074b47323ddb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34c38b3d3f564542956074b47323ddb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34c38b3d3f564542956074b47323ddb5"}}, "title": "Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.", "authors": [{"family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "researcher": {"href": "https://publications.scilifelab.se/researcher/30aece0009c94ace82728640c71682f7.json"}}, {"family": "Oksanen", "given": "Marika", "initials": "M", "orcid": "0000-0003-4140-4282", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a8727638dc49fe88b15052d5741fd5.json"}}, {"family": "Soldini", "given": "Cristina", "initials": "C"}, {"family": "Alatar", "given": "Shemim", "initials": "S", "orcid": "0009-0009-0738-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/0500cee4755b46479d0818314e5c05a7.json"}}, {"family": "Arora", "given": "Abishek", "initials": "A", "orcid": "0000-0002-6149-4417", "researcher": {"href": "https://publications.scilifelab.se/researcher/384ef4f8d6eb49d6873c87556843a7a2.json"}}, {"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Molinari", "given": "Maya", "initials": "M"}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Poulet", "given": "Axel", "initials": "A", "orcid": "0000-0002-3415-8960", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4dfc191bbfd4ed6922008f10531835c.json"}}, {"family": "Watts", "given": "Michelle", "initials": "M", "orcid": "0000-0002-3178-3429", "researcher": {"href": "https://publications.scilifelab.se/researcher/28a00d3b8c3e40e1b68fc333a7aa4fb7.json"}}, {"family": "Rabkina", "given": "Ielyzaveta", "initials": "I", "orcid": "0000-0001-5890-4115", "researcher": {"href": "https://publications.scilifelab.se/researcher/509d3fdbf53b45acbae3ddea4903a0ba.json"}}, {"family": "Becker", "given": "Martin", "initials": "M", "orcid": "0000-0001-8442-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/85eaa4173364473d83506125206a7193.json"}}, {"family": "Li", "given": "Danyang", "initials": "D", "orcid": "0000-0001-7470-6645", "researcher": {"href": "https://publications.scilifelab.se/researcher/01900295a1904ac886960b3eea5915f0.json"}}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM", "orcid": "0000-0002-2488-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/73c8590243874a0a9f18b9e7138ce9a9.json"}}, {"family": "Isaksson", "given": "Johan", "initials": "J", "orcid": "0000-0003-1033-2618", "researcher": {"href": "https://publications.scilifelab.se/researcher/af22620f762a4a5e80dca3f546223caa.json"}}, {"family": "Lundin Remnelius", "given": "Karl", "initials": "K"}, {"family": "Moslem", "given": "Mohsen", "initials": "M"}, {"family": "Jacob", "given": "Yannick", "initials": "Y", "orcid": "0000-0003-4741-0755", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f553bc5034e4768bad65bf8b1236e6a.json"}}, {"family": "Falk", "given": "Anna", "initials": "A", "orcid": "0000-0003-1634-8610", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b708dfb7f0548589bdee53d6e6b536e.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Santini", "given": "Emanuela", "initials": "E", "orcid": "0000-0002-8948-9652", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d176892d0f14922bab782fe4cd69e90.json"}}, {"family": "Borgkvist", "given": "Anders", "initials": "A", "orcid": "0000-0003-1698-0288", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c0f5180d7a74249bcfeb59386a7c65d.json"}}, {"family": "B\u00f6lte", "given": "Sven", "initials": "S", "orcid": "0000-0002-4579-4970", "researcher": {"href": "https://publications.scilifelab.se/researcher/bead50319cae447f90bcf7658d9edf56.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "journal article", "published": "2023-10-15", "journal": {"title": "Biol Open", "issn": "2046-6390", "volume": "12", "issue": "10", "issn-l": "2046-6390"}, "abstract": "Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level HNRNPU downregulation leads to an increased fraction of neural progenitors in the maturing neuronal population. We conclude that the HNRNPU locus is involved in delayed commitment of neural progenitors to differentiate in cell types with hindbrain profile.", "doi": "10.1242/bio.060113", "pmid": "37815090", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10581386"}, {"db": "pii", "key": "330791"}], "notes": [], "created": "2023-11-16T12:03:03.393Z", "modified": "2024-01-16T13:48:31.943Z"}, {"entity": "publication", "iuid": "6448eef2b2ba45f08ede2ebd059ea9d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6448eef2b2ba45f08ede2ebd059ea9d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6448eef2b2ba45f08ede2ebd059ea9d8"}}, "title": "FRET-FISH probes chromatin compaction at individual genomic loci in single cells.", "authors": [{"family": "Mota", "given": "Ana", "initials": "A", "orcid": "0000-0001-8592-9764", "researcher": {"href": "https://publications.scilifelab.se/researcher/508960cbe03d4490a6e4594fc76e3510.json"}}, {"family": "Berezicki", "given": "Szymon", "initials": "S", "orcid": "0000-0003-3980-6290", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8794ceeb3bf405a8125545b49f7ebc7.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Li-Wang", "given": "Xiaoze", "initials": "X"}, {"family": "Gradin", "given": "Katarina", "initials": "K"}, {"family": "Peuckert", "given": "Christiane", "initials": "C"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2022-11-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "6680"}, "abstract": "Chromatin compaction is a key biophysical property that influences multiple DNA transactions. Lack of chromatin accessibility is frequently used as proxy for chromatin compaction. However, we currently lack tools for directly probing chromatin compaction at individual genomic loci. To fill this gap, here we present FRET-FISH, a method combining fluorescence resonance energy transfer (FRET) with DNA fluorescence in situ hybridization (FISH) to probe chromatin compaction at select loci in single cells. We first validate FRET-FISH by comparing it with ATAC-seq, demonstrating that local compaction and accessibility are strongly correlated. FRET-FISH also detects expected differences in compaction upon treatment with drugs perturbing global chromatin condensation. We then leverage FRET-FISH to study local chromatin compaction on the active and inactive X chromosome, along the nuclear radius, in different cell cycle phases, and during increasing passage number. FRET-FISH is a robust tool for probing local chromatin compaction in single cells.", "doi": "10.1038/s41467-022-34183-y", "pmid": "36335096", "labels": {"Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9637210"}, {"db": "pii", "key": "10.1038/s41467-022-34183-y"}], "notes": [], "created": "2023-06-26T12:49:38.233Z", "modified": "2023-11-29T16:29:33.698Z"}, {"entity": "publication", "iuid": "26b36e84d7ee4479848b114b7c51ba21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26b36e84d7ee4479848b114b7c51ba21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26b36e84d7ee4479848b114b7c51ba21"}}, "title": "An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.", "authors": [{"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM", "orcid": "0000-0002-9827-9497", "researcher": {"href": "https://publications.scilifelab.se/researcher/7933c49c5e6448408159ddb654286127.json"}}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "dataset", "published": "2022-07-12", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "9", "issue": "1", "pages": "400"}, "abstract": "Endogenous DNA double-strand breaks (DSBs) occurring in neural cells have been implicated in the pathogenesis of neurodevelopmental disorders (NDDs). Currently, a genomic map of endogenous DSBs arising during human neurogenesis is missing. Here, we applied in-suspension Breaks Labeling In Situ and Sequencing (sBLISS), RNA-Seq, and Hi-C to chart the genomic landscape of DSBs and relate it to gene expression and genome architecture in 2D cultures of human neuroepithelial stem cells (NES), neural progenitor cells (NPC), and post-mitotic neural cells (NEU). Endogenous DSBs were enriched at the promoter and along the gene body of transcriptionally active genes, at the borders of topologically associating domains (TADs), and around chromatin loop anchors. NDD risk genes harbored significantly more DSBs in comparison to other protein-coding genes, especially in NEU cells. We provide sBLISS, RNA-Seq, and Hi-C datasets for each differentiation stage, and all the scripts needed to reproduce our analyses. Our datasets and tools represent a unique resource that can be harnessed to investigate the role of genome fragility in the pathogenesis of NDDs.", "doi": "10.1038/s41597-022-01508-x", "pmid": "35821502", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9276747"}, {"db": "pii", "key": "10.1038/s41597-022-01508-x"}], "notes": [], "created": "2022-08-19T08:38:43.514Z", "modified": "2023-10-16T11:44:09.152Z"}, {"entity": "publication", "iuid": "05430c40833b4be3b4985f41f27377d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05430c40833b4be3b4985f41f27377d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05430c40833b4be3b4985f41f27377d6"}}, "title": "Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.", "authors": [{"family": "Mota", "given": "Ana", "initials": "A", "orcid": "0000-0001-8592-9764", "researcher": {"href": "https://publications.scilifelab.se/researcher/508960cbe03d4490a6e4594fc76e3510.json"}}, {"family": "Schweitzer", "given": "Maud", "initials": "M"}, {"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M"}], "type": "dataset", "published": "2022-02-10", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "9", "issue": "1", "pages": "47", "issn-l": "2052-4463"}, "abstract": "Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62-73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms.", "doi": "10.1038/s41597-022-01139-2", "pmid": "35145120", "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC8831585"}, {"db": "pii", "key": "10.1038/s41597-022-01139-2"}], "notes": [], "created": "2023-06-26T12:49:04.953Z", "modified": "2023-06-26T12:49:05.083Z"}, {"entity": "publication", "iuid": "f9f4da192abc41a59c7dbafd427b7cd0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9f4da192abc41a59c7dbafd427b7cd0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9f4da192abc41a59c7dbafd427b7cd0"}}, "title": "Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study.", "authors": [{"family": "Zerdes", "given": "Ioannis", "initials": "I", "orcid": "0000-0002-8304-2462", "researcher": {"href": "https://publications.scilifelab.se/researcher/f786763a4a0e4b5bb865ebb199eb6ca2.json"}}, {"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Matikas", "given": "Alexios", "initials": "A", "orcid": "0000-0002-4122-9624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0af6483a77d746c2b838414692f1f4ed.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Acs", "given": "Balazs", "initials": "B"}, {"family": "Boyaci", "given": "Ceren", "initials": "C", "orcid": "0000-0001-5598-0243", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1a803107a224c578bf01ef65aba69ff.json"}}, {"family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3fdde99294d422694c7a8a00c9811ed.json"}}, {"family": "Salgkamis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0002-3020-0359", "researcher": {"href": "https://publications.scilifelab.se/researcher/826836fefcf5440ebef1c404e046a0ca.json"}}, {"family": "Agartz", "given": "Susanne", "initials": "S"}, {"family": "Moreno-Ruiz", "given": "Pablo", "initials": "P"}, {"family": "Bai", "given": "Yalai", "initials": "Y"}, {"family": "Rimm", "given": "David L", "initials": "DL", "orcid": "0000-0001-5820-4397", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bb1180d52564c48876ecc4b7e635d52.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A", "orcid": "0000-0002-4394-2634", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd907ed1df0441b99789d3e045c4d890.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd38f4f7704144ed9e3f869e197175e6.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Foukakis", "given": "Theodoros", "initials": "T", "orcid": "0000-0001-8952-9987", "researcher": {"href": "https://publications.scilifelab.se/researcher/7683c0280e9b4145aa54305fb08936a7.json"}}], "type": "journal article", "published": "2021-11-19", "journal": {"title": "NPJ Breast Cancer", "issn": "2374-4677", "volume": "7", "issue": "1", "pages": "144", "issn-l": null}, "abstract": "Emerging data indicate that genomic alterations can shape immune cell composition in early breast cancer. However, there is a need for complementary imaging and sequencing methods for the quantitative assessment of combined somatic copy number alteration (SCNA) and immune profiling in pathological samples. Here, we tested the feasibility of three approaches-CUTseq, for high-throughput low-input SCNA profiling, multiplexed fluorescent immunohistochemistry (mfIHC) and digital-image analysis (DIA) for quantitative immuno-profiling- in archival formalin-fixed paraffin-embedded (FFPE) tissue samples from patients enrolled in the randomized SBG-2004-1 phase II trial. CUTseq was able to reproducibly identify amplification and deletion events with a resolution of 100 kb using only 6 ng of DNA extracted from FFPE tissue and pooling together 77 samples into the same sequencing library. In the same samples, mfIHC revealed that CD4 + T-cells and CD68 + macrophages were the most abundant immune cells and they mostly expressed PD-L1 and PD-1. Combined analysis showed that the SCNA burden was inversely associated with lymphocytic infiltration. Our results set the basis for further applications of CUTseq, mfIHC and DIA to larger cohorts of early breast cancer patients.", "doi": "10.1038/s41523-021-00352-3", "pmid": "34799582", "labels": {"Clinical Genomics Stockholm": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41523-021-00352-3"}, {"db": "pmc", "key": "PMC8604966"}], "notes": [], "created": "2021-12-01T19:52:21.708Z", "modified": "2024-01-16T13:48:38.062Z"}, {"entity": "publication", "iuid": "e18b31942e41465999c590cac3365408", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e18b31942e41465999c590cac3365408.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e18b31942e41465999c590cac3365408"}}, "title": "COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.", "authors": [{"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3fdde99294d422694c7a8a00c9811ed.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Milia", "given": "Maria Grazia", "initials": "MG"}, {"family": "Brossa", "given": "Silvia", "initials": "S"}, {"family": "Huong Nguyen", "given": "Thi Thu", "initials": "TT", "orcid": "0000-0002-9089-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/57451410c8ac4547a4b09111a020e396.json"}}, {"family": "Cerutti", "given": "Francesco", "initials": "F", "orcid": "0000-0003-0480-8296", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a243dc846624a8a8292dde5416fa402.json"}}, {"family": "Berrino", "given": "Enrico", "initials": "E"}, {"family": "Sapino", "given": "Anna", "initials": "A"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Sottile", "given": "Antonino", "initials": "A"}, {"family": "Ghisetti", "given": "Valeria", "initials": "V", "orcid": "0000-0002-4698-598X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75237266d0b1496f909cb0c53ff87920.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2021-06-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3903", "issn-l": "2041-1723"}, "abstract": "While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.", "doi": "10.1038/s41467-021-24078-9", "pmid": "34162869", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-24078-9"}, {"db": "pmc", "key": "PMC8222401"}], "notes": [], "created": "2021-10-01T09:02:30.491Z", "modified": "2024-01-16T13:48:39.472Z"}, {"entity": "publication", "iuid": "d71873c329c7421db086762eddcf7cb7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d71873c329c7421db086762eddcf7cb7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d71873c329c7421db086762eddcf7cb7"}}, "title": "GPSeq reveals the radial organization of chromatin in the cell nucleus.", "authors": [{"family": "Girelli", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-4264-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/a607510e88954d0980e1d4505ab27ee7.json"}}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Kallas", "given": "Tomasz", "initials": "T"}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Spanjaard", "given": "Bastiaan", "initials": "B"}, {"family": "Mota", "given": "Ana", "initials": "A"}, {"family": "Kolbeinsdottir", "given": "Solrun", "initials": "S"}, {"family": "Gelali", "given": "Eleni", "initials": "E", "orcid": "0000-0003-0067-5473", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1a4d90932dd45509d71a672ec5a12af.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "38", "issue": "10", "pages": "1184-1193", "issn-l": "1087-0156"}, "abstract": "With the exception of lamina-associated domains, the radial organization of chromatin in mammalian cells remains largely unexplored. Here we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius. GPSeq relies on gradual restriction digestion of chromatin from the nuclear lamina toward the nucleus center, followed by sequencing of the generated cut sites. Using GPSeq, we mapped the radial organization of the human genome at 100-kb resolution, which revealed radial patterns of genomic and epigenomic features and gene expression, as well as A and B subcompartments. By combining radial information with chromosome contact frequencies measured by Hi-C, we substantially improved the accuracy of whole-genome structure modeling. Finally, we charted the radial topography of DNA double-strand breaks, germline variants and cancer mutations and found that they have distinctive radial arrangements in A and B subcompartments. We conclude that GPSeq can reveal fundamental aspects of genome architecture.", "doi": "10.1038/s41587-020-0519-y", "pmid": "32451505", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-0519-y"}, {"db": "pmc", "key": "PMC7610410"}, {"db": "mid", "key": "EMS118404"}], "notes": [], "created": "2020-05-26T07:12:39.312Z", "modified": "2021-11-10T12:46:51.496Z"}]}