EXPERIMENT_TITLE: GSM6198803: H3K56; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For crosslinking, the cells suspension was treated with formaldehyde at a final concentration of 1% (H3K56/vol) and incubated for 10 min at room temperature, followed by quenching with 0.125 M glycine for 5 min at room temperature. After pelleted through 1,000 g for 5 min at 4 °C, the harvested cells were washed twice with ice cold PBS, aliquoted to 20 million aliquots per 1.5 ml Eppendorf tube, and stored at -80 °C for further delivery to Novogene Com., Beijing for Hi-C library generation. Hi-C library generation was conducted by Novogene Com., Beijing.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: A generalizable strategy with programmable site-specificity for in situ profiling of histone modifications on unperturbed chromatin remains highly desirable but challenging. We herein developed a Single-site-resolved multi-omics (SiTomics) strategy for systematic mapping of dynamic modifications, and subsequent profiling of chromatinized proteome and genome defined by specific chromatin acylations in living cells. By leveraging the genetic code expansion strategy, our SiTomics toolkit revealed distinct crotonylation (e.g., H3K56cr) and ß-hydroxybutyrylation (e.g., H3K56bhb) upon short chain fatty acids stimulation, and established linkages for chromatin acylation mark-defined proteome, genome and functions. This led to the identification of GLYR1 as a distinct interacting protein in modulating H3K56cr's gene body localization as well as the discovery of an elevated super-enhancer repertoire underlying bhb-mediated chromatin modulations. SiTomics offers a platform technology for elucidating the “metabolites-modification-regulation” axis, which is widely applicable for multi-omics profiling and functional dissection of modifications beyond acylations and proteins beyond histones. Overall design: Hi-C was performed to explore the 3D genome changes caused by site-specific histone acylations
SAMPLE_TITLE: H3K56
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HEK293T cells"}, {"TAG": "histone", "VALUE": "WT-H3(H3K56)"}]
Pool_Member_@attributes_sample_title: H3K56
RUN_SET_RUN_Pool_Member_@attributes_sample_title: H3K56
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