EXPERIMENT_TITLE: GSM3356360: Hi-C, T990275; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C experiments were performed by Arima Genomics (https://arimagenomics.com/) utilizing a single restriction enzyme and multiple restriction enzymes for chromatin digestion. After the HiC protocol, Illumina-compatible sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting DNA fragments from ~200-600bp using SPRI beads. The size-selected fragments were then enriched for biotin, and converted into Illumina-compatible sequencing libraries with TruSeq adapters using the KAPA Hyper Prep kit. After adapter ligation, DNA was PCR amplified with Illumina primers and library fragments of ~525 bp (insert plus adaptor) were purified using SPRI beads. The purified DNA underwent standard QC (qPCR and Bioanalyzer) and sequenced on the Illumina HiSeq 3000 instrument following the manufacturer's protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: H3K27ac paired-end NanoChIP-seq, whole-genome sequecing, RNA-seq and Hi-C were integrated to reveal tumor-associated structural variants contributing to gastric cancer Overall design: Hi-C profiles were generated to interrogate for chromatin interactions and topological-associated domains.
SAMPLE_TITLE: Hi-C, T990275
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "gastric cancer primary sample"}, {"TAG": "sample id", "VALUE": "T990275"}, {"TAG": "tissue/cell type", "VALUE": "gastric cancer primary sample"}]
Pool_Member_@attributes_sample_title: Hi-C, T990275
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