{"entity": "journal", "iuid": "4c94803328904243a643b0202f5e2ddc", "timestamp": "2026-06-09T02:33:59.988Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/J.%20Histochem.%20Cytochem..json"}, "display": {"href": "https://publications.scilifelab.se/journal/J.%20Histochem.%20Cytochem."}}, "title": "J. Histochem. Cytochem.", "issn": "1551-5044", "issn-l": "0022-1554", "publications_count": 7, "publications": [{"entity": "publication", "iuid": "8d950590445341e6a83dd636c0171874", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d950590445341e6a83dd636c0171874.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d950590445341e6a83dd636c0171874"}}, "title": "Making Multiplexed Imaging Flexible: Combining Essential Markers With Established Antibody Panels.", "authors": [{"family": "Deen", "given": "Ashik Jawahar", "initials": "AJ", "orcid": "0000-0002-8200-6849", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c59fa0cba5d4da0819bbf41998f33e0.json"}}, {"family": "Thorsson", "given": "Johan", "initials": "J"}, {"family": "O'Roberts", "given": "Eleanor M", "initials": "EM", "orcid": "0000-0002-5375-459X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5472fa88ba584d54952d2f1581ebd48a.json"}}, {"family": "Panshikar", "given": "Pranauti", "initials": "P", "orcid": "0009-0003-6239-6952", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5a7aeb9efec4840bb1d761a2e3597f4.json"}}, {"family": "Ullman", "given": "Tony", "initials": "T", "orcid": "0009-0001-4865-5925", "researcher": {"href": "https://publications.scilifelab.se/researcher/d167706b90c84b01a987132f301a247a.json"}}, {"family": "Krantz", "given": "David", "initials": "D"}, {"family": "Oses", "given": "Carolina", "initials": "C"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}], "type": "journal article", "published": "2024-08-31", "journal": {"title": "J. Histochem. Cytochem.", "issn": "1551-5044", "issn-l": "0022-1554", "volume": "72", "issue": "8-9", "pages": "517-544"}, "abstract": "Multiplexed immunofluorescence (IF) can be achieved using different commercially available platforms, often making use of conjugated antibodies detected in iterative cycles. A growing portfolio of pre-conjugated antibodies is offered by the providers, as well as the possibility for in-house conjugation. For many conjugation methods and kits, there are limitations in which antibodies can be used, and conjugation results are sometimes irreproducible. The conjugation process can limit or slow down the progress of studies requiring conjugation of essential markers needed for a given project. Here, we demonstrate a protocol combining manual indirect immunofluorescence (IF) of primary antibodies, followed by antibody elution and staining with multiplexed panels of commercially pre-conjugated antibodies on the PhenoCycler platform. We present detailed protocols for applying the workflow on fresh frozen and formalin fixed paraffin embedded tissue sections. We also provide a ready to use workflow for coregistration of the images and demonstrate this for two examples.", "doi": "10.1369/00221554241274856", "pmid": "39215640", "labels": {"BioImage Informatics": "Service", "Spatial Proteomics": "Technology development", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11421402"}], "notes": [], "created": "2024-11-13T09:53:21.828Z", "modified": "2025-01-22T09:31:34.703Z"}, {"entity": "publication", "iuid": "d23f81c368e94e89aaf7b3ffaf6f29bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d23f81c368e94e89aaf7b3ffaf6f29bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d23f81c368e94e89aaf7b3ffaf6f29bc"}}, "title": "Heparan Sulfate Biosynthesis in Zebrafish.", "authors": [{"family": "Filipek-G\u00f3rniok", "given": "Beata", "initials": "B", "orcid": "0000-0002-6757-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f0b7b3e0b045f082d2aff1dd23ec0e.json"}}, {"family": "Habicher", "given": "Judith", "initials": "J"}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}, {"family": "Kjell\u00e9n", "given": "Lena", "initials": "L"}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "J. Histochem. Cytochem.", "issn": "1551-5044", "volume": "69", "issue": "1", "pages": "49-60", "issn-l": "0022-1554"}, "abstract": "The biosynthesis of heparan sulfate (HS) proteoglycans occurs in the Golgi compartment of cells and will determine the sulfation pattern of HS chains, which in turn will have a large impact on the biological activity of the proteoglycans. Earlier studies in mice have demonstrated the importance of HS for embryonic development. In this review, the enzymes participating in zebrafish HS biosynthesis, along with a description of enzyme mutants available for functional studies, are presented. The consequences of the zebrafish genome duplication and maternal transcript contribution are briefly discussed as are the possibilities of CRISPR/Cas9 methodologies to use the zebrafish model system for studies of biosynthesis as well as proteoglycan biology.", "doi": "10.1369/0022155420973980", "pmid": "33216642", "labels": {"Genome Engineering Zebrafish": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7780192"}], "notes": [], "created": "2021-01-12T09:33:36.164Z", "modified": "2021-11-10T12:28:04.027Z"}, {"entity": "publication", "iuid": "10d32e326ad143b48c7352913a9537b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10d32e326ad143b48c7352913a9537b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10d32e326ad143b48c7352913a9537b3"}}, "title": "A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface.", "authors": [{"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Kugel", "given": "Laura", "initials": "L"}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Aslan", "given": "Joseph E", "initials": "JE"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "J. Histochem. Cytochem.", "issn": "1551-5044", "issn-l": "0022-1554", "volume": "68", "issue": "7", "pages": "473-489"}, "abstract": "Imaging is a powerful approach for studying protein expression and has the advantage over other methodologies in providing spatial information in situ at single cell level. Using immunofluorescence and confocal microscopy, detailed information of subcellular distribution of proteins can be obtained. While adherent cells of different tissue origin are relatively easy to prepare for imaging applications, non-adherent cells from hematopoietic origin, present a challenge due to their poor attachment to surfaces and subsequent loss of a substantial fraction of the cells. Still, these cell types represent an important part of the human proteome and express genes that are not expressed in adherent cell types. In the era of cell mapping efforts, overcoming the challenge with suspension cells for imaging applications would enable systematic profiling of hematopoietic cells. In this work, we successfully established an immunofluorescence protocol for preparation of suspension cell lines, peripheral blood mononucleated cells (PBMC) and human platelets on an adherent surface. The protocol is based on a multi-well plate format with automated sample preparation, allowing for robust high throughput imaging applications. In combination with confocal microscopy, the protocol enables systematic exploration of protein localization to all major subcellular structures.", "doi": "10.1369/0022155420935403", "pmid": "32564662", "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC7350080"}], "notes": [], "created": "2020-01-07T15:30:10.784Z", "modified": "2021-12-09T13:58:56.335Z"}, {"entity": "publication", "iuid": "c8efe8a2a2534aa1a79059542fa9c9ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8efe8a2a2534aa1a79059542fa9c9ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8efe8a2a2534aa1a79059542fa9c9ff"}}, "title": "A Systematic Characterization of Aquaporin-9 Expression in Human Normal and Pathological Tissues.", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Catrina", "given": "Anca", "initials": "A"}, {"family": "Nielsen", "given": "S\u00f8ren", "initials": "S"}, {"family": "R\u00fctzler", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2016-05-00", "journal": {"volume": "64", "issn": "1551-5044", "issue": "5", "pages": "287-300", "title": "J. Histochem. Cytochem.", "issn-l": "0022-1554"}, "abstract": "AQP9 is known to facilitate hepatocyte glycerol uptake. Murine AQP9 protein expression has been verified in liver, skin, epididymis, epidermis and neuronal cells using knockout mice. Further expression sites have been reported in humans. We aimed to verify AQP9 expression in a large set of human normal organs, different cancer types, rheumatoid arthritis synovial biopsies as well as in cell lines and primary cells. Combining standardized immunohistochemistry with high-throughput mRNA sequencing, we found that AQP9 expression in normal tissues was limited, with high membranous expression only in hepatocytes. In cancer tissues, AQP9 expression was mainly found in hepatocellular carcinomas, suggesting no general contribution of AQP9 to carcinogenesis. AQP9 expression in a subset of rheumatoid arthritis synovial tissue samples was affected by Humira, thereby supporting a suggested role of TNF\u03b1 in AQP9 regulation in this disease. Among cell lines and primary cells, LP-1 myeloma cells expressed high levels of AQP9, whereas low expression was observed in a few other lymphoid cell lines. AQP9 mRNA and protein expression was absent in HepG2 hepatocellular carcinoma cells. Overall, AQP9 expression in human tissues appears to be more selective than in mice.", "doi": "10.1369/0022155416641028", "pmid": "27026296", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "0022155416641028"}, {"db": "pmc", "key": "PMC4851273"}], "notes": [], "created": "2017-05-03T12:59:21.114Z", "modified": "2017-11-05T13:07:39.915Z"}, {"entity": "publication", "iuid": "9b379261e5574a0cbfc364715c570bfc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b379261e5574a0cbfc364715c570bfc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b379261e5574a0cbfc364715c570bfc"}}, "title": "Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling.", "authors": [{"family": "Edqvist", "given": "Per-Henrik D", "initials": "PH"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-02-00", "journal": {"volume": "63", "issn": "1551-5044", "issue": "2", "pages": "129-141", "title": "J. Histochem. Cytochem.", "issn-l": "0022-1554"}, "abstract": "To increase our understanding of skin, it is important to define the molecular constituents of the cell types and epidermal layers that signify normal skin. We have combined a genome-wide transcriptomics analysis, using deep sequencing of mRNA from skin biopsies, with immunohistochemistry-based protein profiling to characterize the landscape of gene and protein expression in normal human skin. The transcriptomics and protein expression data of skin were compared to 26 (RNA) and 44 (protein) other normal tissue types. All 20,050 putative protein-coding genes were classified into categories based on patterns of expression. We found that 417 genes showed elevated expression in skin, with 106 genes expressed at least five-fold higher than that in other tissues. The 106 genes categorized as skin enriched encoded for well-known proteins involved in epidermal differentiation and proteins with unknown functions and expression patterns in skin, including the C1orf68 protein, which showed the highest relative enrichment in skin. In conclusion, we have applied a genome-wide analysis to identify the human skin-specific proteome and map the precise localization of the corresponding proteins in different compartments of the skin, to facilitate further functional studies to explore the molecular repertoire of normal skin and to identify biomarkers related to various skin diseases.", "doi": "10.1369/0022155414562646", "pmid": "25411189", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "0022155414562646"}, {"db": "pmc", "key": "PMC4305515"}], "notes": [], "created": "2017-05-02T12:56:54.324Z", "modified": "2021-07-08T13:44:33.465Z"}, {"entity": "publication", "iuid": "9bc18320f3eb4b8c84a460c382604ee3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bc18320f3eb4b8c84a460c382604ee3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bc18320f3eb4b8c84a460c382604ee3"}}, "title": "Antibodies biotinylated using a synthetic Z-domain from protein A provide stringent in situ protein detection.", "authors": [{"family": "Andersson", "given": "Sandra", "initials": "S"}, {"family": "Konrad", "given": "Anna", "initials": "A"}, {"family": "Ashok", "given": "Nikhil", "initials": "N"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Asplund", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "61", "issn": "1551-5044", "issue": "11", "pages": "773-784", "title": "J. Histochem. Cytochem.", "issn-l": "0022-1554"}, "abstract": "Antibody-based protein profiling on a global scale using immunohistochemistry constitutes an emerging strategy for mapping of the human proteome, which is crucial for an increased understanding of biological processes in the cell. Immunohistochemistry is often performed indirectly using secondary antibodies for detection, with the benefit of signal amplification. Direct immunohistochemistry instead brings the advantage of multiplexing; however, it requires labeling of the primary antibody. Many antibody-labeling kits do not specifically target IgG and may therefore cause labeling of stabilizing proteins present in the antibody solution. A new conjugation method has been developed that utilizes a modified Z-domain of protein A (ZBPA) to specifically target the Fc part of antibodies. The aim of the present study was to compare the ZBPA conjugation method and a commercially available labeling kit, Lightning-Link, for in situ protein detection. Fourteen antibodies were biotinylated with each method and stained using immunohistochemistry. For all antibodies tested, ZBPA biotinylation resulted in distinct immunoreactivity without off-target staining, regardless of the presence of stabilizing proteins in the buffer, whereas the majority of the Lightning-Link biotinylated antibodies displayed a characteristic pattern of nonspecific staining. We conclude that biotinylated ZBPA domain provides a stringent method for antibody biotinylation, advantageous for in situ protein detection in tissues.", "doi": "10.1369/0022155413502360", "pmid": "23920108", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "0022155413502360"}, {"db": "pmc", "key": "PMC3808578"}], "notes": [], "created": "2017-05-04T14:55:59.857Z", "modified": "2017-05-30T12:55:44.005Z"}, {"entity": "publication", "iuid": "edae7ecf86524014a794009823055c99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edae7ecf86524014a794009823055c99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edae7ecf86524014a794009823055c99"}}, "title": "The impact of tissue fixatives on morphology and antibody-based protein profiling in tissues and cells.", "authors": [{"family": "Paavilainen", "given": "Linda", "initials": "L"}, {"family": "Edvinsson", "given": "Asa", "initials": "A"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}], "type": "comparative study", "published": "2010-03-00", "journal": {"volume": "58", "issn": "1551-5044", "issue": "3", "pages": "237-246", "title": "J. Histochem. Cytochem.", "issn-l": "0022-1554"}, "abstract": "Pathology archives harbor large amounts of formalin-fixed, paraffin-embedded tissue samples, used mainly in clinical diagnostics but also for research purposes. Introduction of heat-induced antigen retrieval has enabled the use of tissue samples for extensive immunohistochemical analysis, despite the fact that antigen retrieval may not recover all epitopes, owing to alterations of the native protein structure induced by formalin. The aim of this study was to investigate how different fixatives influence protein recognition by immunodetection methods in tissues, cell preparations, and protein lysates, as compared with formalin. Seventy-two affinity-purified polyclonal antibodies were used to evaluate seven different fixatives. The aldehyde-based fixative Glyo-fixx proved to be excellent for preservation of proteins in tissue detected by immunohistochemistry (IHC), similar to formalin. A non-aldehyde-based fixative, NEO-FIX was superior for fixation of cultured cells, in regard to morphology, and thereby also advantageous for IHC. Large variability in the amount of protein extracted from the differently fixed tissues was observed, and the HOPE fixative provided the overall highest yield of protein. In conclusion, morphological resolution and immunoreactivity were superior in tissues fixed with aldehyde-based fixatives, whereas the use of non-aldehyde-based fixatives can be advantageous in obtaining high protein yield for Western blot analysis. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.", "doi": "10.1369/jhc.2009.954321", "pmid": "19901271", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "jhc.2009.954321"}, {"db": "pmc", "key": "PMC2825489"}], "notes": [], "created": "2017-05-04T14:55:43.381Z", "modified": "2017-05-30T12:58:03.697Z"}], "created": "2017-05-09T09:12:06.733Z", "modified": "2020-11-27T13:14:05.241Z"}