EXPERIMENT_TITLE: GSM4908640: LUAD_tissue2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Disrupt the frozen tissue(20-40 mg ) either by coarsely chopping it with a razor blade on a petri dish placed on dry ice or by grinding it with a mortar and pestle in liquid nitrogen. Then Transfer the disrupted tissue samples to a 1.5 mL microcentrifuge tube which contain 1 ml 1X PBS and 40.5µl 37% formaldehyde, then vortexing the tube for 30s to mix and rotating tube at room temperature for 20 min. Pipeting off and discard the supernatant and washing the pellet with 300 µl wash buffer, after the second wash, added to pellet (99 µl Wash Buffer;1 µl 40 mM Calcium Chloride ;25 µl 1 mg/mL Collagenase), then incubate it for 1 hour at 37°C in an agitating thermal mixer (1250 rpm). After incubation, add 6.3 µl 20% SDS to the sample, then pipet up and down to break up any large clumps, after briefly vortex to resuspend, transfer the SUPERNATANT to a new 1.5 mL microcentrifuge tube. the sample was fixed with formaldehyde, and the intracellular protein was cross-linked with DNA, the cross-linked cells were lysed and digested with DpnII, filled with biotin-14-dATP, proximately ligated with T4 DNA ligase and reverse crosslinked with 5M sodium chloride. Then the genome DNA was purified, sheared and size-selected. Biotin pull-down was performed to enrich target DNA fragments, followed by standard Illumina library construction, lastly using a TapeStation or Bioanalyzer to verify the size distribution of your size-selected library.Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We report the application of Hi-C technology for high-throughput profiling of LUAD and normal tissues. By obtaining over three billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of LUAD. We found the main conversion type of compartment is A?B in tumor tissues, 216 tumor-specific TADs and 41 distinct enhancer-promoter loops in tumor tissue. And these chromatin structure variations are mainly on chromosome 3. We also found 5 most important genes (SYT16, NCEH1, NXPE3, MB21D2, and DZIP1L), which were detected in both A?B compartment, TADs and chromatin loops. Overall design: Examination of LUAD and paired normal tissues of 2 patients
SAMPLE_TITLE: LUAD_tissue2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "cancer tissue"}, {"TAG": "tissue", "VALUE": "lung adenocarcinoma"}, {"TAG": "tumor stage", "VALUE": "stage III"}, {"TAG": "treatment", "VALUE": "untreated"}]
Pool_Member_@attributes_sample_title: LUAD_tissue2
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