EXPERIMENT_TITLE: GSM3336894: Hi-C TAMR Replicate 2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were cross-linked with formaldehyde, lysed and the intact nuclei was permeabilized. DNA was then cut with NcolI restriction enzyme, the overhangs filled in incorporating a biotinylated base and the free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and the biotinylated ligation junctions were pulled down with streptavidin beads. Custom library construction protocol was followed. Briefly, DNA was end-repaired and dA-tailing using the NEBNext DNA Master Mixes kit and the ligation of universal adapter was performed on Streptavidin-bound DNA using the NEBNext Ultra DNA Library Prep kit. After adapter ligation DNA was PCR amplified with indexed Illumina primers for 8-12 cycles and library fragments of at least 200bp were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Endocrine therapy resistance invariably develops in estrogen receptor positive (ER+) breast cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that 3-dimensional (3D) chromatin interactions both within and between topologically associating domains (TADs) frequently change in ER+ endocrine resistant breast cancer cells and that the differential interactions are enriched for genetic variants at CTCF-bound anchors. Ectopic chromatin interactions are preferentially enriched at active enhancers and promoters and ER binding sites and are associated with altered expression of ER-regulated genes, consistent with dynamic remodelling of ER pathways accompanying the development of endocrine resistance. Importantly, new 3D chromatin interactions often occur coincidently with hypermethylation and loss of ER binding. Additionally, alterations in active (A-type) and inactive (B-type) chromosomal compartments are also associated with decreased ER binding and atypical interactions and gene expression. Together, our results suggest that 3D epigenome remodelling is a key mechanism underlying endocrine resistance in ER+ breast cancer. Overall design: Hi-C, WGS, WGBS, ChIP-seq and RNA-seq were conducted in endocrine-sensitive breast cancer cells (MCF7) and its two endocrine-resistant derivatives - tamoxifen-resistant (TAMR) cells and fulvestrant-resistant (FASR) cells.
SAMPLE_TITLE: Hi-C TAMR Replicate 2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "TAMR"}, {"TAG": "cell line", "VALUE": "MCF7"}, {"TAG": "cell type", "VALUE": "breast cancer cells"}, {"TAG": "resistant phenotype", "VALUE": "tamoxifen-resistant"}]
Pool_Member_@attributes_sample_title: Hi-C TAMR Replicate 2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C TAMR Replicate 2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TKCC_TAMR_NcolII_2_R1.fastq.gz", "size": "9775933821", "date": "2020-02-19 15:36:52", "md5": "27b04f7a45b3ab60294fd7149dce1e76", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TKCC_TAMR_NcolII_2_R2.fastq.gz", "size": "10062196662", "date": "2020-02-19 15:36:52", "md5": "c52c0b46dfe84edd8cfabf3752aac702", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7707711", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7707711/SRR7707711", "size": "14446460725", "date": "2018-08-17 17:01:36", "md5": "01d9c6451f0a90ba3b6ba2286ccf79b0", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7707711.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR007/707/SRR7707711.sralite.1", "size": "8305091749", "date": "2020-06-22 09:43:39", "md5": "8beaf7517ba0d8764bf916618909b205", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]