{"entity": "researcher", "timestamp": "2026-07-20T00:25:34.277Z", "family": "Yoshihara", "given": "Masahito", "initials": "M", "orcid": "0000-0002-8915-9282", "affiliations": ["Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/4303ab7a18254bb59f8e2386a7f7fb0a.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/4303ab7a18254bb59f8e2386a7f7fb0a"}}, "publications": [{"entity": "publication", "iuid": "af16f7f2a5004801bdd004545bd190b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af16f7f2a5004801bdd004545bd190b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af16f7f2a5004801bdd004545bd190b9"}}, "title": "The DoGA consortium expression atlas of promoters and genes in 100 canine tissues.", "authors": [{"family": "H\u00f6rtenhuber", "given": "Matthias", "initials": "M", "orcid": "0000-0002-5599-5565", "researcher": {"href": "https://publications.scilifelab.se/researcher/a02296c8f90742c6a9de21e12359560c.json"}}, {"family": "Hyt\u00f6nen", "given": "Marjo K", "initials": "MK", "orcid": "0000-0003-1976-5874", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e3788ab09f415f918f0bf9ed441fac.json"}}, {"family": "Mukarram", "given": "Abdul Kadir", "initials": "AK"}, {"family": "Arumilli", "given": "Meharji", "initials": "M"}, {"family": "Araujo", "given": "C\u00e9sar L", "initials": "CL"}, {"family": "Quintero", "given": "Ileana", "initials": "I", "orcid": "0000-0001-7040-1289", "researcher": {"href": "https://publications.scilifelab.se/researcher/208e9727fc004f10acca1e3ed3244366.json"}}, {"family": "Syrj\u00e4", "given": "Pernilla", "initials": "P"}, {"family": "Airas", "given": "Niina", "initials": "N"}, {"family": "Kaukonen", "given": "Maria", "initials": "M", "orcid": "0000-0002-2146-4694", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4e0e0816a714e72976563c625549785.json"}}, {"family": "Ky\u00f6stil\u00e4", "given": "Kaisa", "initials": "K"}, {"family": "Niskanen", "given": "Julia", "initials": "J", "orcid": "0000-0002-2871-6890", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c9070b3a4bb4b9f93f85caf587b2b98.json"}}, {"family": "Jokinen", "given": "Tarja S", "initials": "TS", "orcid": "0000-0001-6389-0109", "researcher": {"href": "https://publications.scilifelab.se/researcher/435d360e63f94f48831777352c2e1d9a.json"}}, {"family": "Mottaghitalab", "given": "Faezeh", "initials": "F", "orcid": "0000-0001-6495-6667", "researcher": {"href": "https://publications.scilifelab.se/researcher/faed0b7f48c144de81c6720b9866b50f.json"}}, {"family": "Takan", "given": "I\u015f\u0131l", "initials": "I", "orcid": "0000-0002-0269-6625", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7c6daf8dc524e21a2d44de764146965.json"}}, {"family": "Salokorpi", "given": "Noora", "initials": "N"}, {"family": "Raman", "given": "Amitha", "initials": "A"}, {"family": "Stevens", "given": "Irene", "initials": "I", "orcid": "0000-0003-3823-1499", "researcher": {"href": "https://publications.scilifelab.se/researcher/90f6fa81197146ae946e2f68630c1238.json"}}, {"family": "Iivanainen", "given": "Antti", "initials": "A", "orcid": "0000-0003-1002-3225", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f39943341f5457986553f672841ae04.json"}}, {"family": "Yoshihara", "given": "Masahito", "initials": "M", "orcid": "0000-0002-8915-9282", "researcher": {"href": "https://publications.scilifelab.se/researcher/4303ab7a18254bb59f8e2386a7f7fb0a.json"}}, {"family": "Gusev", "given": "Oleg", "initials": "O", "orcid": "0000-0002-6203-9758", "researcher": {"href": "https://publications.scilifelab.se/researcher/31d4a1b245d449428a6fe219c91cde24.json"}}, {"family": "Bannasch", "given": "Danika", "initials": "D", "orcid": "0000-0002-7614-7207", "researcher": {"href": "https://publications.scilifelab.se/researcher/828a952f3be54507bedcb950fbafaf12.json"}}, {"family": "Sukura", "given": "Antti", "initials": "A", "orcid": "0000-0002-8992-1695", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea53fec228424344bd642575de25aec3.json"}}, {"family": "Schoenebeck", "given": "Jeffrey J", "initials": "JJ", "orcid": "0000-0003-4964-2138", "researcher": {"href": "https://publications.scilifelab.se/researcher/674777750c7144d783483e2c8f130b8b.json"}}, {"family": "DoGA Consortium", "given": "", "initials": ""}, {"family": "Ezer", "given": "Sini", "initials": "S"}, {"family": "Katayama", "given": "Shintaro", "initials": "S", "orcid": "0000-0001-7581-5157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7765acd351b40c091615258c3d751b4.json"}}, {"family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications.scilifelab.se/researcher/eda6a90f9d9046ada163d9843d169393.json"}}, {"family": "Kere", "given": "Juha", "initials": "J", "orcid": "0000-0003-1974-0271", "researcher": {"href": "https://publications.scilifelab.se/researcher/102085fb1c3147ceaf8dcb7651df1303.json"}}, {"family": "Lohi", "given": "Hannes", "initials": "H", "orcid": "0000-0003-1087-5532", "researcher": {"href": "https://publications.scilifelab.se/researcher/903f658d43ea414fb37ef530df3e15e4.json"}}], "type": "journal article", "published": "2024-10-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9082", "issn-l": "2041-1723"}, "abstract": "The dog, Canis lupus familiaris, is an important model for studying human diseases. Unlike many model organisms, the dog genome has a comparatively poor functional annotation, which hampers gene discovery for development, morphology, disease, and behavior. To fill this gap, we established a comprehensive tissue biobank for both the dog and wolf samples. The biobank consists of 5485 samples representing 132 tissues from 13 dogs, 12 dog embryos, and 24 wolves. In a subset of 100 tissues from nine dogs and 12 embryos, we characterized gene expression activity for each promoter, including alternative and novel, i.e., previously not annotated, promoter regions, using the 5' targeting RNA sequencing technology STRT2-seq. We identified over 100,000 promoter region candidates in the recent canine genome assembly, CanFam4, including over 45,000 highly reproducible sites with gene expression and respective tissue enrichment levels. We provide a promoter and gene expression atlas with interactive, open data resources, including a data coordination center and genome browser track hubs. We demonstrated the applicability of Dog Genome Annotation (DoGA) data and resources using multiple examples spanning canine embryonic development, morphology and behavior, and diseases across species.", "doi": "10.1038/s41467-024-52798-1", "pmid": "39433728", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11494170"}, {"db": "pii", "key": "10.1038/s41467-024-52798-1"}], "notes": [], "created": "2025-02-28T14:14:28.582Z", "modified": "2025-02-28T14:14:29.644Z"}, {"entity": "publication", "iuid": "a223b2180f754d79971096d57b714ee6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a223b2180f754d79971096d57b714ee6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a223b2180f754d79971096d57b714ee6"}}, "title": "Single-cell analysis of human ovarian cortex identifies distinct cell populations but no oogonial stem cells.", "authors": [{"family": "Wagner", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-6266-1248", "researcher": {"href": "https://publications.scilifelab.se/researcher/124ac27397f845a68732369680da7c5a.json"}}, {"family": "Yoshihara", "given": "Masahito", "initials": "M", "orcid": "0000-0002-8915-9282", "researcher": {"href": "https://publications.scilifelab.se/researcher/4303ab7a18254bb59f8e2386a7f7fb0a.json"}}, {"family": "Douagi", "given": "Iyadh", "initials": "I", "orcid": "0000-0002-3221-8667", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a19504ddb2544bca5aeab9abf885b13.json"}}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Panula", "given": "Sarita", "initials": "S"}, {"family": "Petropoulos", "given": "Sophie", "initials": "S"}, {"family": "Lu", "given": "Haojiang", "initials": "H"}, {"family": "Pettersson", "given": "Karin", "initials": "K"}, {"family": "Palm", "given": "Kerstin", "initials": "K"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Hovatta", "given": "Outi", "initials": "O", "orcid": "0000-0001-5395-3807", "researcher": {"href": "https://publications.scilifelab.se/researcher/f822ca12dfe0462b99c06e57cace4ce0.json"}}, {"family": "Kere", "given": "Juha", "initials": "J", "orcid": "0000-0003-1974-0271", "researcher": {"href": "https://publications.scilifelab.se/researcher/102085fb1c3147ceaf8dcb7651df1303.json"}}, {"family": "Lanner", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-2771-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba53ce48a35d413eb86cd104488ce669.json"}}, {"family": "Damdimopoulou", "given": "Pauliina", "initials": "P", "orcid": "0000-0001-8458-0855", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d258c0f0d9b417ea4608769fc3ebaaf.json"}}], "type": "journal article", "published": "2020-03-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "1147", "issn-l": "2041-1723"}, "abstract": "The human ovary orchestrates sex hormone production and undergoes monthly structural changes to release mature oocytes. The outer lining of the ovary (cortex) has a key role in defining fertility in women as it harbors the ovarian reserve. It has been postulated that putative oogonial stem cells exist in the ovarian cortex and that these can be captured by DDX4 antibody isolation. Here, we report single-cell transcriptomes and cell surface antigen profiles of over 24,000 cells from high quality ovarian cortex samples from 21 patients. Our data identify transcriptional profiles of six main cell types; oocytes, granulosa cells, immune cells, endothelial cells, perivascular cells, and stromal cells. Cells captured by DDX4 antibody are perivascular cells, not oogonial stem cells. Our data do not support the existence of germline stem cells in adult human ovaries, thereby reinforcing the dogma of a limited ovarian reserve.", "doi": "10.1038/s41467-020-14936-3", "pmid": "32123174", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-14936-3"}, {"db": "pmc", "key": "PMC7052271"}], "notes": [], "created": "2020-03-03T10:20:08.878Z", "modified": "2024-01-16T13:48:42.834Z"}]}