Project description:A deeper understanding of the biology of therapy resistant cells is important for the development of optimal therapeutic strategies to attain complete cure of leukemia. Here we compared chromatin accessibility of CML patient cells treated with Imatinib vs untreated cells and column enriched deep-quiescent LI (leukemia initiator) cells. ICG-001 treatment of LIs suggested increased differentiation of LIs.
Project description:Alterations in RNA Polymerase II kinetics can affect key co-transcriptional processes such as normal splicing and transcript elongation and can influence nonsense mediated decay (Fong et al., 2014; Jonkers and Lis, 2015). Specific types of DNA damage can variably influence RNA Pol II activity. We performed Total RNA Pol ll ChIP-seq to investigate how the chronic DNA damage can affect RNA Pol ll activity in the cerebellum tissues.
2021-12-14 | GSE176511 | GEO
Project description:Lentiviral integration site sequencing (LIS-seq)
Project description:Alterations in RNA Polymerase II kinetics can affect key co-transcriptional processes such as normal splicing and transcript elongation and can influence nonsense mediated decay (Fong et al., 2014; Jonkers and Lis, 2015). Specific types of DNA damage can variably influence RNA Pol II activity. Thus, we performed RNA Pol ll pSer5 ChIP-seq to investigate how the chronic DNA damage can affect to RNA Pol ll activity in the cerebellum tissues.
Project description:The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications. Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nuclear matrix respectively. We have mapped, by array CGH, the locations of attachment to each of these residual protein bodies relative to non-attached DNA along the entire length of human chromosomes 14, 15, 16, 17 and 18 in HeLa cells. LIS or 2 M NaCl solutions followed by restriction digestion with EcoR1 facilitates the separation from scaffold/matrix bound DNA from non bound DNA. Genomic CGH arrays were used to map the relative differences between attached (scaffold/matrix) and non-attached (loop) portions of HeLa DNA. The expression profile of the HeLa cells used for aCGH analysis was also determined.
Project description:The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications. Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nuclear matrix respectively. We have mapped, by array CGH, the locations of attachment to each of these residual protein bodies relative to non-attached DNA along the entire length of human chromosomes 14, 15, 16, 17 and 18 in AoAF cells. LIS (lithium 3,5-diiodosalicylate) or 2 M NaCl solutions followed by restriction digestion with EcoR1 facilitates the separation from scaffold/matrix bound DNA from non bound DNA. Genomic CGH arrays were used to map the relative differences between attached (scaffold/matrix) and non-attached (loop) portions of AoAF DNA. The expression profile of the AoAF cells used for aCGH analysis was determined.
Project description:The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications. Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nuclear matrix respectively. We have mapped, by array CGH, the locations of attachment to each of these residual protein bodies relative to non-attached DNA along the entire length of human chromosomes 14, 15, 16, 17 and 18 in HeLa cells.
Project description:The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications. Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nuclear matrix respectively. We have mapped, by array CGH, the locations of attachment to each of these residual protein bodies relative to non-attached DNA along the entire length of human chromosomes 14, 15, 16, 17 and 18 in AoAF cells.