EXPERIMENT_TITLE: GSM4969660: NHA-HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C in cell and tissue was performed following the manufacturer's protocol (A510008, Arima Genomics). Cells were cultured and crosslinked using 1% formaldehyde for 10 minutes and quenched with 0.125M glycine for five minutes at RT. A total of 3 million cells were used for each Hi-C experiment. Tissue samples were frozen with liquid nitrogen and pulverized using mortar and pestle until the sample resembles a fine powder, then crosslinked using the same condition as cell lines. Hi-C libraries were generated and quality checked per manufacturer's protocol. 300-600M reads per each sample was generated based on total usable reads above 20Kb.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are highly morbid childhood brain tumors. Even with treatment, overall 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 proteins. To investigate whether this H3K27M mutation 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 mutant and wild-type specimens, we identified tumor specific enhancers and regulatory networks for known oncogenes. In addition, we identified distinct genomic structural variations that lead to enhancer hijacking and gene co-amplification, including A2M, JAG2, FLRT1. Overall design: RNA-Seq, ChIP-Seq for H3K27ac, H3K27me3, and H3K27M, ATAC-seq and genome-wide chromatin conformation capture (Hi-C) in patient-derived cell lines (DIPG n=6, GBM n=3, normal n=2) and frozen tissue specimens (DIPG n=1 normal brainstem n=1). Note from submitter: we are unable to upload the A3810-raw data files because of privacy issues with human samples.
SAMPLE_TITLE: NHA-HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "NHA"}, {"TAG": "chip-antibody", "VALUE": "NA"}]
Pool_Member_@attributes_sample_title: NHA-HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: NHA-HiC
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