EXPERIMENT_TITLE: GSM8036105: BT-549,Ctrl,day2,hic,rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Following cellular cross-linking with 1% formaldehyde and nuclei extraction in hypotonic solution, the genomic DNA was digested with restriction enzyme MboI (NEB) at 37 °C overnight and labelled with biotinylated nucleotides when the cohesive ends were filled. Then, blunt-end proximity ligation was performed with T4 DNA ligase (NEB) at 16 °C for 4 h. After decrosslinking with proteinase K (Thermo) at 65°C overnight, ligated DNA was purified by QIAamp DNA Mini Kit (Qiagen) and sheared to ~400 bp. Next, Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen) was used to pull down the biotin-marked ligation junctions. Purified DNA was used to prepare ChIP-seq DNA libraries for Illumina sequencing by KAPA Hyper Prep Kit (KAPABIOSYSTEMS) according to the manufacturer's instructions. The Hi-C library was generated using NEBNext Ultra™ II DNA library Prep Kit (NEB) according to the manufacturer's instructions.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To investigate the Nexturastat A effects on chromatin structure which disrupt phospho-HDAC6 LLPS in triple-negative breast cancer (TNBC), we conducted the analysis of Hi-C in TNBC cells treated with or without Nexturastat A. Overall design: control group:untreat BT-549. treatment group: 5uM Nexturastat A treated BT-549 for 2 days
SAMPLE_TITLE: BT-549,Ctrl,day2,hic,rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "BT-549"}, {"TAG": "cell line", "VALUE": "BT-549"}, {"TAG": "cell type", "VALUE": "Epithelial cell, Breast, Triple-negative"}, {"TAG": "treatment", "VALUE": "DMSO"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: BT-549,Ctrl,day2,hic,rep1
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