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- Forrest, ARR, et al.
(författare)
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A promoter-level mammalian expression atlas
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 507:7493, s. 462-
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Iannelli, F, et al.
(författare)
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A damaged genome's transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks
- 2017
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8, s. 15656-
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Tidskriftsartikel (refereegranskat)abstract
- Of the many types of DNA damage, DNA double-strand breaks (DSBs) are probably the most deleterious. Mounting evidence points to an intricate relationship between DSBs and transcription. A cell system in which the impact on transcription can be investigated at precisely mapped genomic DSBs is essential to study this relationship. Here in a human cell line, we map genome-wide and at high resolution the DSBs induced by a restriction enzyme, and we characterize their impact on gene expression by four independent approaches by monitoring steady-state RNA levels, rates of RNA synthesis, transcription initiation and RNA polymerase II elongation. We consistently observe transcriptional repression in proximity to DSBs. Downregulation of transcription depends on ATM kinase activity and on the distance from the DSB. Our study couples for the first time, to the best of our knowledge, high-resolution mapping of DSBs with multilayered transcriptomics to dissect the events shaping gene expression after DSB induction at multiple endogenous sites.
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| 6. |
- Mitteldorf, C., et al.
(författare)
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Expression of programmed death-1 (CD279) in primary cutaneous B-cell lymphomas with correlation to lymphoma entities and biological behaviour
- 2013
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Ingår i: British Journal of Dermatology. - : Blackwell Publishing Ltd. - 0007-0963 .- 1365-2133. ; 169:6, s. 1212-1218
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Tidskriftsartikel (refereegranskat)abstract
- Background Programmed death-1 (PD-1/CD279) is a cell-surface protein expressed in activated T cells and a subset of T lymphocytes including follicular helper T cells (TFH). The interaction between PD-1 and its ligands plays a role in immune response and evasion of malignancies. In nodal follicular lymphoma, the number of intratumoral PD-1-positive lymphocytes is associated with overall survival. Objectives To investigate 28 cases of primary cutaneous B-cell lymphoma, including the subtypes PCFCL (n = 10), PCMZL (n = 10) and DLBCL-LT (n = 8) for the number and density of PD-1-positive cells. Methods Immunohistochemical staining and a computerized morphometric analysis for evaluation were applied. The results were correlated with the clinical outcome. To distinguish between activated T cells and TFH we performed PD-1/bcl-6 double staining and compared these results with CXCL-13 staining. Double staining for PD-1 and PAX-5 was used to investigate whether tumour cells were positive for PD-1. Results The PD-1-positive cells represented tumour-infiltrating T cells (TILs). Only a minor subset was represented by TFH. Patients with DLBCL-LT had a significantly lower number of PD-1-positive TILs than those with PCMZL (P = 0·012) and PCFCL (P = 0·002) or both (P = 0·001). The difference between PCMZL and PCFCL did not reach significance (P = 0·074). The tumour cells were negative for PD-1. Conclusions A higher number of PD-1-expressing cells was found in indolent PCMZL and PCFCL than in high-malignant DLBCL-LT. The PD-1-positive cells represented not only TFH, but also other activated T cells as a part of the tumour microenvironment. The tumour cells in all investigated types of PCBCL did not show aberrant PD-1 expression. What’s already known about this topic? In nodal follicular lymphoma, the number of intratumoral programmed death (PD)-1-positive lymphocytes is associated with overall survival. No data exist for primary cutaneous B-cell lymphoma (PCBCL). What does this study add? A higher number of PD-1-expressing cells was found in indolent primary cutaneous marginal zone lymphoma and primary cutaneous follicle centre lymphoma, in contrast to the more aggressive diffuse large B-cell lymphoma, leg type. PD-1-positive cells do not represent only follicular helper T cells. The tumour cells in all investigated types of PCBCL did not show aberrant PD-1 expression. © 2013 British Association of Dermatologists.
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| 7. |
- Voskuil, Jan L. A., et al.
(författare)
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The Antibody Society's antibody validation webinar series
- 2020
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Ingår i: mAbs. - : Informa UK Limited. - 1942-0862 .- 1942-0870. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- In the wake of the reproducibility crisis and numerous discussions on how commercially available antibodies as research tool contribute to it, The Antibody Society developed a series of 10 webinars to address the issues involved. The webinars were delivered by speakers with both academic and commercial backgrounds. This report highlights the problems, and offers solutions to help the scientific community appropriately identify the right antibodies and to validate them for their research and development projects. Despite the various solutions proposed here, they must be applied on a case-by-case basis. Each antibody must be verified based on the content of the product sheet, and subsequently through experimentation to confirm integrity, specificity and selectivity. Verification needs to focus on the precise application and tissue/cell type for which the antibody will be used, and all verification data must be reported openly. The various approaches discussed here all have caveats, so a combination of solutions must be considered.
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