Core Unit C will assist the individual projects by providing the following functions :1) Genome-wide profiling of DNase I Hypersensitive Sites (DHSs). In support of Project 1, Core Unit C will profile the DHSs of fetal human erythroid cells and adult CD34 cell-derived erythroblasts and will provide the data from all other lineages and cell lines required for the identification of the insulator elements of the human genome. In support of Project 2, the unit will profile the DHSs of the thalassemia-derived iPS cells and the erythroid cells derived from differentiation of IPS cells. In support of Project 4, the Unit will provide access to comprehensive data on DHS in human hemopoietic cells to be used to further characterize the correlation between VIS and DHS in the setting of clinical samples. 2) Genome-wide mapping of specific protein-DNA binding sites (Chip-seq). In support of Project 1, Genomics Core Unit C will perform the high-throughput sequencing associated with the genome-wide ChlP-seq analysis of USF1/2 and CTCF binding sites. This will include the ligation of P5 and P7 primers, template amplification, sequencing on the Solexa platform, mapping of sequence tags, and calculation of binding hotspots. 3) Assisting with the informatics and automated cloning and sequencing needs. Core Unit C will provide assistance with informatics needs related to genomics analysis in support of all projects as they develop during the course of the PPG. This will include in part the mapping and correlation of VIS and genomics properties in support of Project 4, and the correlation between several genomics properties related to the identification of candidate chromatin insulators in support of Project 1. The Core Unit will also provide assistance with physical aspects of automated cloning and sequencing in support of all projects as they develop during the course of this PPG.
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| Gori, Jennifer L; Butler, Jason M; Kunar, Balvir et al. (2017) Endothelial Cells Promote Expansion of Long-Term Engrafting Marrow Hematopoietic Stem and Progenitor Cells in Primates. Stem Cells Transl Med 6:864-876 |
| Psatha, Nikoletta; Karponi, Garyfalia; Yannaki, Evangelia (2016) Optimizing autologous cell grafts to improve stem cell gene therapy. Exp Hematol 44:528-39 |
| Li, Li B; Ma, Chao; Awong, Geneve et al. (2016) Silent IL2RG Gene Editing in Human Pluripotent Stem Cells. Mol Ther 24:582-91 |
| Karponi, Garyfalia; Psatha, Nikoletta; Lederer, Carsten Werner et al. (2015) Plerixafor+G-CSF-mobilized CD34+ cells represent an optimal graft source for thalassemia gene therapy. Blood 126:616-9 |
| Vierstra, Jeff; Reik, Andreas; Chang, Kai-Hsin et al. (2015) Functional footprinting of regulatory DNA. Nat Methods 12:927-30 |
| Qi, Heyuan; Liu, Mingdong; Emery, David W et al. (2015) Functional validation of a constitutive autonomous silencer element. PLoS One 10:e0124588 |
| Liu, Mingdong; Maurano, Matthew T; Wang, Hao et al. (2015) Genomic discovery of potent chromatin insulators for human gene therapy. Nat Biotechnol 33:198-203 |
| Polak, Paz; Karli?, Rosa; Koren, Amnon et al. (2015) Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature 518:360-364 |
| Chandrasekaran, Devikha; Nakamoto, Betty; Watts, Korashon L et al. (2014) Modeling promising nonmyeloablative conditioning regimens in nonhuman primates. Hum Gene Ther 25:1013-22 |
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