EXPERIMENT_TITLE: GSM5556552: HiC_KO1_2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C data was generated from 1M WT, CTCF +/- #1 or CTCF +/- #2 MCF10A cells per replicates, with 2 replicates per conditions, using the Arima-HiC kit, according to the manufacturer's protocols (Arima Genomics). Library preparation was performed using KAPA Hyper Prep Kit  (#07962312001) following Arima protocol for library preparation.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Epigenetic mechanisms often play an important role in driving tumor progression towards metastasis. It is less clear that deregulation of chromatin architecture, including topologically associated domains (TADS), contributes to cancer progression. CTCF is a central regulator of three dimensional chromatin structure that undergoes copy number loss in over half of all breast cancers, but the impact of this defect on epigenetic programming and chromatin architecture remains obscure. We find that the reduced pools of CTCF in hemizygous models potentiates cell invasion. Underlying this phenotype is the activation of oncogenic networks including the PI3K signaling cascade, which presents therapeutic vulnerabilities, especially to mTOR inhibitors. Deregulation of these oncogenic pathways is largely due to the loss of CTCF insulation, allowing a reorganization of long-range chromatin contacts at the subTAD level that is associated with aberrant programming of H3K27 acetylation at enhancer/promoter regions. Thus, lowered CTCF levels lead to chromatin reorganization facilitating pro-invasive transcriptional programs. Overall design: Examination of mRNA expression, CTCF binding, H3K4me3, H3K27ac, DNA Methylation and chromatin conformation underlying the oncogenic phenotypes potentiated by CTCF LOH in mammalian breast epithelial cells.
SAMPLE_TITLE: HiC_KO1_2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "CTCF +/- #1 MCF10A"}, {"TAG": "tissue", "VALUE": "Breast"}, {"TAG": "cell type", "VALUE": "MCF10A"}, {"TAG": "genotype", "VALUE": "CTCF +/-"}]
Pool_Member_@attributes_sample_title: HiC_KO1_2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_KO1_2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15712679.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR015/15712/SRR15712679/SRR15712679.lite.1", "size": "7679823560", "date": "2022-09-01 02:12:23", "md5": "67e6861986398e8b6296b4b614785045", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15712679", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15712679/SRR15712679", "size": "9334261220", "date": "2021-09-04 08:23:19", "md5": "59082ed31e3d09b5bde84aa4fc64cc7b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_KO1_2_R2.fastq.gz", "size": "8121531013", "date": "2021-09-04 08:18:48", "md5": "3f6cf0604813b0cc7f94e782ebc8f6a4", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_KO1_2_R1.fastq.gz", "size": "7823584324", "date": "2021-09-04 08:19:38", "md5": "e4178212171945d2258e5ca201113402", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]