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Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are morbid brain tumors. Even with treatment survival is poor, making pHGG the number one cause of cancer death in children. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding histone H3. To investigate whether H3K27M is associated with distinct chromatin structure that alters transcription regulation, we generated the first high-resolution Hi-C maps of pHGG cell lines and tumor tissue. By integrating transcriptome (RNA-seq), enhancer landscape (ChIP-seq), genome structure (Hi-C), and chromatin accessibility (ATAC-seq) datasets from H3K27M and wild-type specimens, we identified tumor-specific enhancers and regulatory networks for known oncogenes. We identified genomic structural variations that lead to potential enhancer hijacking and gene coamplification, including A2M , JAG2 , and FLRT1 . Together, our results imply three-dimensional genome a ....
The Ionic FFPE Complete Purification Kit is used with the Ionic system to enable the automated purification of DNA and RNA, including microRNA from FFPE tissue samples. The kit provides a protocol, Ionic ® Fluidic Chips and reagents to enable the Ionic system to automate DNA and RNA purification using an innovative isotachophoresis technology. Samples are prepared for purification on the Ionic system using a simple lysis procedure that can be automated u ....