EXPERIMENT_TITLE: GSM4696930: KYSE180_H3K27acHiChIP_1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: HiChIP was done as previously described (Mumbach et al., 2016) with minor changes. Libraries were prepared using the KAPA HyperPrep kit according to the manufacturer's manual. HiChIP
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Using an unbiased method, we found a testis-specific epigenetic reader protein BRDT to be expressed and functional active in a significant portion of ESCC patients. Mechanistically, BRDT co-localizes with ?Np63, a defining transcription factor for squamous subtype, at selected super-enhancers to regulate ?Np63-dependent transcription programs to promote cell migration. Pharmacologically depleting BRDT resembles the effects of knock-down of BRDT, thus providing a promising clinical approach for precision medicine in a subset of ESCC. Overall design: Examination of H3K27ac-associated chromatin interaction in ESCC.
SAMPLE_TITLE: KYSE180_H3K27acHiChIP_1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Esophageal squamous cell carcinoma"}, {"TAG": "cell line", "VALUE": "ESCC cell line KYSE180"}, {"TAG": "chip antibody", "VALUE": "H3K27ac (Diagenode, C15410196)"}, {"TAG": "treatment", "VALUE": "non-targeting siRNA"}]
Pool_Member_@attributes_sample_title: KYSE180_H3K27acHiChIP_1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: KYSE180_H3K27acHiChIP_1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "KYSE180_H3K27ac_HiChIP_1_R1.fastq.gz", "size": "1552285914", "date": "2020-07-27 15:24:07", "md5": "a3bd7b96f4a3da10e70b06248567ca61", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "KYSE180_H3K27ac_HiChIP_1_R2.fastq.gz", "size": "1818968502", "date": "2020-07-27 15:24:41", "md5": "730af1b80e9e581730de230c4f7d5403", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR12331554", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12331554/SRR12331554", "size": "2530111715", "date": "2020-07-27 15:26:46", "md5": "f1467110a6dd172a50c501477831a373", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR12331554.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR012/12331/SRR12331554/SRR12331554.lite.1", "size": "1556540451", "date": "2022-07-18 11:06:33", "md5": "d92c9673cfb63368af52189ea4131d80", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]