Relevant bibliographies by topics / 3D DNA FISH

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters

Academic literature on the topic '3D DNA FISH'

Author: Grafiati
Published: 4 June 2021
Last updated: 8 February 2022

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Journal articles on the topic "3D DNA FISH"

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Ortiz de Solorzano, C., K. Chin, D. Knowles, et al. "3d Confocal Microscopy and Image Analysis for Measurement of Genetic Instability." Microscopy and Microanalysis 5, S2 (1999): 1022–23. http://dx.doi.org/10.1017/s1431927600018432.

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Solid tumors frequently contain cells that are heterogeneous in the copy number of DNA loci. This fact implies the existence of genetic instability, which may be associated with disease aggressiveness. Accurate measurement of this phenomenon requires analysis of intact nuclei within their natural tissue context. We perform these measurements by preparing >30μm thick tissue sections, labeling them with fluorescent labels for total DNA and for specific DNA loci using fluorescence in situ hybridization (FISH) which retain the transparency of the tissue and acquiring 3D images of the tissue usi
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Kulasinghe, Arutha, Yenkai Lim, Joanna Kapeleris, Majid Warkiani, Ken O’Byrne, and Chamindie Punyadeera. "The Use of Three-Dimensional DNA Fluorescent In Situ Hybridization (3D DNA FISH) for the Detection of Anaplastic Lymphoma Kinase (ALK) in Non-Small Cell Lung Cancer (NSCLC) Circulating Tumor Cells." Cells 9, no. 6 (2020): 1465. http://dx.doi.org/10.3390/cells9061465.

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Tumor tissue biopsy is often limited for non-small cell lung cancer (NSCLC) patients and alternative sources of tumoral information are desirable to determine molecular alterations such as anaplastic lymphoma kinase (ALK) rearrangements. Circulating tumor cells (CTCs) are an appealing component of liquid biopsies, which can be sampled serially over the course of treatment. In this study, we enrolled a cohort of ALK-positive (n = 8) and ALK-negative (n = 12) NSCLC patients, enriched for CTCs using spiral microfluidic technology and performed DNA fluorescent in situ hybridization (FISH) for ALK.
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Muller, S., M. Neusser, D. Kohler, and M. Cremer. "Preparation of Complex DNA Probe Sets for 3D FISH with up to Six Different Fluorochromes." Cold Spring Harbor Protocols 2007, no. 10 (2007): pdb.prot4730. http://dx.doi.org/10.1101/pdb.prot4730.

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Weber, Patrick, Cathia Rausch, Annina Scholl, and M. Cristina Cardoso. "Repli-FISH (Fluorescence in Situ Hybridization): Application of 3D-(Immuno)-FISH for the Study of DNA Replication Timing of Genetic Repeat Elements." OBM Genetics 3, no. 1 (2018): 1. http://dx.doi.org/10.21926/obm.genet.1901062.

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Zenk, Fides, Yinxiu Zhan, Pavel Kos, et al. "HP1 drives de novo 3D genome reorganization in early Drosophila embryos." Nature 593, no. 7858 (2021): 289–93. http://dx.doi.org/10.1038/s41586-021-03460-z.

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AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein
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Němečková, Alžběta, Christina Wäsch, Veit Schubert, Takayoshi Ishii, Eva Hřibová, and Andreas Houben. "CRISPR/Cas9-Based RGEN-ISL Allows the Simultaneous and Specific Visualization of Proteins, DNA Repeats, and Sites of DNA Replication." Cytogenetic and Genome Research 159, no. 1 (2019): 48–53. http://dx.doi.org/10.1159/000502600.

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Visualizing the spatiotemporal organization of the genome will improve our understanding of how chromatin structure and function are intertwined. Here, we describe a further development of the CRISPR/Cas9-based RNA-guided endonuclease-in situ labeling (RGEN-ISL) method. RGEN-ISL allowed the differentiation between vertebrate-type (TTAGGG)n and Arabidopsis-type (TTTAGGG)n telomere repeats. Using maize as an example, we established a combination of RGEN-ISL, immunostaining, and EdU labeling to visualize in situ specific repeats, histone marks, and DNA replication sites, respectively. The effects
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Liu, Guanqing, and Tao Zhang. "Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation." International Journal of Molecular Sciences 22, no. 13 (2021): 7124. http://dx.doi.org/10.3390/ijms22137124.

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Oligonucleotides fluorescence in situ hybridization (Oligo-FISH) is an emerging technology and is an important tool in research areas such as detection of chromosome variation, identification of allopolyploid, and deciphering of three-dimensional (3D) genome structures. Based on the demand for highly efficient oligo probes for oligo-FISH experiments, increasing numbers of tools have been developed for probe design in recent years. Obsolete oligonucleotide design tools have been adapted for oligo-FISH probe design because of their similar considerations. With the development of DNA sequencing a
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Zha, Mengsheng, Nan Wang, Chaoyang Zhang, and Zheng Wang. "Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential." International Journal of Molecular Sciences 22, no. 11 (2021): 5914. http://dx.doi.org/10.3390/ijms22115914.

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Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single-cell Hi-C contact matrices. We designed a novel loss function based on
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Lockett, S. J., D. W. Knowles, D. Pinkel, and C. Ortiz de Solórzano. "Quantitative 3d Analysis Of Intra-Nuclear Organization In The Tissue Context." Microscopy and Microanalysis 5, S2 (1999): 1320–21. http://dx.doi.org/10.1017/s1431927600019929.

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Confocal microscopy is revealing associations between the internal organization of the nucleus and tissue architecture and function. Such associations may exist which are too subtle or complex for visual observation or quantitative analysis may be required, for example as input data to mathematical modeling of cellular processes. In these circumstances, it is necessary to perform the analysis using computer algorithms. We have developed 3D image analysis (IA) algorithms for segmenting nuclei from within intact tissue specimens, measuring the structure of the nuclei and for segmenting specifica
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Knecht, Hans, Narisorn Kongruttanachok, Bassem Sawan, Zelda Lichtensztejn, Daniel Lichtensztejn, and Sabine Mai. "3D Telomere Dynamics In Hodgkin's Lymphoma." Blood 116, no. 21 (2010): 745. http://dx.doi.org/10.1182/blood.v116.21.745.745.

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Abstract Abstract 745 Introduction: Innovative 3D telomere q-FISH allows a mechanistic understanding of the transition from the mononuclear Hodgkin (H) to the multinuclear Reed-Sternberg (RS) cell in in Hodgkin's lymphoma (HL) derived cell lines and diagnostic patient biopsies (Leukemia. 2009; 23:565-573). In RS-cells the telomere protecting shelterin complex appears to be disrupted and deregulation of DNA repair mechanisms is observed. These changes occur in both, classical EBV negative and EBV-associated, LMP1 expressing HL (Lab Invest. 2010; 90:611-619). However, it is not known whether the
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Dissertations / Theses on the topic "3D DNA FISH"

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Marti, Marimon Maria Eugenia. "3D genome conformation and gene expression in fetal pig muscle at late gestation." Thesis, Toulouse, INPT, 2018. http://www.theses.fr/2018INPT0099.

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Dans le secteur de l’élevage porcin, les truies ont été sélectionnées pendant des décennies pour leur prolificité afin de maximiser la production de viande. Cependant, cette sélection a été associée à une mortalité plus élevée des nouveau-nés. Dans ce contexte, le muscle foetal squelettique est essentiel à la survie du porcelet, car il est nécessaire pour les fonctions motrices et la thermorégulation. Par ailleurs, la structure tridimensionnelle du génome s'est avérée jouer un rôle important dans la régulation de l'expression génique. Ainsi, dans ce projet, nous nous sommes intéressés à la con
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Book chapters on the topic "3D DNA FISH"

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Jubb, Alasdair, and Shelagh Boyle. "Visualizing Genome Reorganization Using 3D DNA FISH." In Methods in Molecular Biology. Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0623-0_5.

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Lucic, Bojana, Julia Wegner, Mia Stanic, Katharina Laurence Jost, and Marina Lusic. "3D Immuno-DNA Fluorescence In Situ Hybridization (FISH) for Detection of HIV-1 and Cellular Genes in Primary CD4+ T Cells." In Methods in Molecular Biology. Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0664-3_14.

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Giorgetti, Luca, Tristan Piolot, and Edith Heard. "High-Resolution 3D DNA FISH Using Plasmid Probes and Computational Correction of Optical Aberrations to Study Chromatin Structure at the Sub-megabase Scale." In Methods in Molecular Biology. Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-2253-6_3.

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Hausmann, Michael, Jin-Ho Lee, and Georg Hildenbrand. "3D DNA FISH for analyses of chromatin-nuclear architecture." In Epigenetics Methods. Elsevier, 2020. http://dx.doi.org/10.1016/b978-0-12-819414-0.00020-3.

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